Journal of Computer - Aided Molecular Design (journal)

published in (P1433)

Q56979331	Q56979331
Q56986646	Q56986646
Q59188930	Q59188930
Q60015703	Q60015703
Q60488592	Q60488592
Q63367548	Q63367548
Q48230076	"In silico" study of the binding of two novel antagonists to the nociceptin receptor
Q52412458	'ValleyScan': a new two-bond drive technique for the calculation of potential energy surfaces with less computational effort
Q35929548	1001 Ways to run AutoDock Vina for virtual screening
Q44667597	2-Pyridone and 3-oxo-1,2,6-thiadiazine-1,1-dioxide derivatives: a new class of hydrogen bond equivalents of uracil
Q62700164	2D and 3D QSAR studies of diarylpyrimidine HIV-1 reverse transcriptase inhibitors
Q41549374	2D- and 3D-QSAR studies of a series of benzopyranes and benzopyrano[3,4b][1,4]-oxazines as inhibitors of the multidrug transporter P-glycoprotein
Q44832225	3-D QSAR analysis of steroid/protein interactions: The use of difference maps
Q40629130	3D QSAR (COMFA) of a series of potent and highly selective VLA-4 antagonists
Q44667589	3D QSAR studies on binding affinities of coumarin natural products for glycosomal GAPDH of Trypanosoma cruzi
Q74665324	3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling
Q43136203	3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents
Q44711407	3D-QSAR and docking studies on 4-anilinoquinazoline and 4-anilinoquinoline epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors
Q78325092	3D-QSAR and molecular modeling of HIV-1 integrase inhibitors
Q81437679	3D-QSAR illusions
Q56979316	3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands
Q42853767	3D-QSAR studies and molecular docking on [5-(4-amino-1H-benzoimidazol-2-yl)-furan-2-yl]-phosphonic acid derivatives as fructose-1,6-biphophatase inhibitors
Q28281913	3D-QSAR study of hallucinogenic phenylalkylamines by using CoMFA approach
Q73013885	3D-QSAR using 'multiconformer' alignment: the use of HASL in the analysis of 5-HT1A thienopyrimidinone ligands
Q33225366	3D-chiral atom, atom-type, and total non-stochastic and stochastic molecular linear indices and their applications to central chirality codification
Q42664052	5,10-Methylene-5,6,7,8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies
Q44968836	5-HT1A receptor pharmacophores to screen for off-target activity of α1-adrenoceptor antagonists.
Q60546489	A 3D QSAR CoMFA study of non-peptide angiotensin II receptor antagonists
Q56978865	A 3D QSAR approach to the search for geometrical similarity in a series of nonpeptide angiotensin II receptor antagonists
Q33195977	A Bayesian molecular interaction library.
Q47415465	A CADD-alog of strategies in pharma
Q73652678	A CoMFA analysis with conformational propensity: an attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method
Q39425242	A D3R prospective evaluation of machine learning for protein-ligand scoring.
Q30349714	A Java applet for multiple linked visualization of protein structure and sequence.
Q36877402	A Monte Carlo method for finding important ligand fragments from receptor data
Q72741855	A Monte Carlo pharmacophore generation procedure: application to the human PAF receptor
Q59188953	A PLS QSAR analysis using 3D generated aromatic descriptors of principal property type: Application to some dopamine D2 benzamide antagonists
Q30355593	A Python tool to set up relative free energy calculations in GROMACS.
Q54329542	A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant.
Q62112721	A QM/MM study of the binding of RAPTA ligands to cathepsin B
Q89949713	A Taxicab geometry quantification system to evaluate the performance of in silico methods: a case study on adenosine receptors ligands
Q92260433	A benchmark study of loop modeling methods applied to G protein-coupled receptors
Q97427563	A binding mode hypothesis for prothioconazole binding to CYP51 derived from first principles quantum chemistry
Q92650830	A blind SAMPL6 challenge: insight into the octanol-water partition coefficients of drug-like molecules via a DFT approach
Q52234490	A branch-and-bound method for optimal atom-type assignment in de novo ligand design.
Q52435968	A case for sharing.
Q34220542	A collaborative environment for developing and validating predictive tools for protein biophysical characteristics
Q47217355	A combined Fisher and Laplacian score for feature selection in QSAR based drug design using compounds with known and unknown activities.
Q30357121	A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist.
Q48054359	A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.
Q77832767	A comparative docking study and the design of potentially selective MMP inhibitors
Q43566210	A comparative molecular field analysis of cytochrome P450 2A5 and 2A6 inhibitors
Q57021674	A comparative molecular similarity index analysis (CoMSIA) study identifies an HLA-A2 binding supermotif
Q43206017	A comparative study of AutoDock and PMF scoring performances, and SAR of 2-substituted pyrazolotriazolopyrimidines and 4-substituted pyrazolopyrimidines as potent xanthine oxidase inhibitors
Q42176495	A comparative study of family-specific protein-ligand complex affinity prediction based on random forest approach
Q33952708	A comparative study of fragment screening methods on the p38α kinase: new methods, new insights
Q77365342	A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors
Q30391442	A comparison of different functions for predicted protein model quality assessment
Q52265017	A comparison of heuristic search algorithms for molecular docking.
Q92612919	A comparison of molecular representations for lipophilicity quantitative structure-property relationships with results from the SAMPL6 logP Prediction Challenge
Q28201523	A comparison of progestin and androgen receptor binding using the CoMFA technique
Q44325912	A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP.
Q80547849	A comprehensive analysis of the thermodynamic events involved in ligand-receptor binding using CoRIA and its variants
Q86826027	A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings
Q43445035	A computational analysis of the binding mode of closantel as inhibitor of the Onchocerca volvulus chitinase: insights on macrofilaricidal drug design
Q34010186	A computational analysis of the binding model of MDM2 with inhibitors
Q36099514	A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis
Q74625543	A computational model of the nicotinic acetylcholine binding site
Q90952063	A computational study of the molecular basis of antibiotic resistance in a DXR mutant
Q71851464	A computational study on the relative reactivity of reductively activated 1,4-benzoquinone and its isoelectronic analogs
Q44912595	A computational tool to optimize ligand selectivity between two similar biomacromolecular targets
Q43122434	A computational workflow for the design of irreversible inhibitors of protein kinases.
Q73913505	A computationally efficient alternative to the Buckingham potential for molecular mechanics calculations
Q38973999	A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation.
Q28282247	A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function
Q45059897	A correlation study of quinoline derivatives and their pharmaceutical behavior by ab initio calculated NQR parameters
Q47820357	A critical assessment of finite element modeling approach for protein dynamics
Q83298882	A critical cross-validation of high throughput structural binding prediction methods for pMHC
Q38610941	A cross docking pipeline for improving pose prediction and virtual screening performance.
Q28654731	A crystallographic perspective on sharing data and knowledge
Q89460089	A deep learning approach for the blind logP prediction in SAMPL6 challenge
Q44770779	A density functional reactivity theory (DFRT) based approach to understand the interaction of cisplatin analogues with protecting agents
Q35345510	A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands.
Q43476760	A fast and efficient method for 2D and 3D molecular shape description
Q34319994	A fast and efficient method to generate biologically relevant conformations
Q52373577	A fast empirical method for the calculation of molecular polarizability.
Q52402049	A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists.
Q52235674	A flexible triangulation method to describe the solvent-accessible surface of biopolymers.
Q57127520	A fragment-based approach to the SAMPL3 Challenge
Q87797011	A functional feature analysis on diverse protein-protein interactions: application for the prediction of binding affinity
Q52321852	A genetic algorithm for flexible molecular overlay and pharmacophore elucidation.
Q43936134	A genetic algorithm for structure-based de novo design
Q52346343	A genetic algorithm for the automated generation of molecules within constraints.
Q52076493	A genetic algorithm for the automated generation of small organic molecules: drug design using an evolutionary algorithm.
Q83845165	A giant's shoulders: a perspective from Professor Norman L. Allinger
Q48517142	A grand vision for configurable science and minimizing the loss model. Interview by Wendy A. Warr.
Q51708836	A graph-theoretic approach to modeling metabolic pathways
Q114689843	A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios
Q44268642	A homology-based model of the human 5-HT2A receptor derived from an in silico activated G-protein coupled receptor
Q38558151	A hybrid approach for addressing ring flexibility in 3D database searching
Q35918516	A k-nearest neighbor classification of hERG K(+) channel blockers
Q51899073	A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers.
Q30367330	A ligand's-eye view of protein binding.
Q41151213	A machine learning approach to computer-aided molecular design
Q51932206	A marriage made in torsional space: using GALAHAD models to drive pharmacophore multiplet searches.
Q51297155	A mechanism-based 3D-QSAR approach for classification and prediction of acetylcholinesterase inhibitory potency of organophosphate and carbamate analogs.
Q44302800	A method for fast energy estimation and visualization of protein-ligand interaction
Q47252192	A model for the binding of low molecular weight inhibitors to the active site of thrombin
Q44490737	A model of the human M2 muscarinic acetylcholine receptor
Q52561640	A modification to the COSMIC parameterisation using ab initio constrained potential functions.
Q54111648	A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery.
Q40311614	A molecular dynamics simulation study decodes the early stage of the disassembly process abolishing the human SAMHD1 function
Q63916879	A molecular graphics study exploring a putative ligand binding site of theβ-adrenoceptor
Q41449034	A molecular graphics study on structure-action relationships of calcium-antagonistic and agonistic 1,4-dihydropyridines
Q46642481	A molecular mechanism of P-loop pliability of Rho-kinase investigated by molecular dynamic simulation
Q46159478	A molecular model for the active site of S-adenosyl-L-homocysteine hydrolase
Q72137023	A molecular model of the folate binding site of Pneumocystis carinii dihydrofolate reductase
Q47655100	A molecular modeling study of inhibitors of nuclear factor kappa-B (p50)--DNA binding
Q69373816	A molecular modeling study on binding of drugs to calmodulin
Q69360064	A molecular modelling study of the interaction of noradrenaline with the beta 2-adrenergic receptor
Q57012728	A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors
Q57012695	A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching
Q40814720	A multivariate insight into the in vitro antitumour screen database of the National Cancer Institute: classification of compounds, similarities among cell lines and the influence of molecular targets.
Q52244277	A multiway 3D QSAR analysis of a series of (S)-N-[(1-ethyl-2-pyrrolidinyl)methyl]-6-methoxybenzamides.
Q72741849	A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces
Q41812083	A new fingerprint to predict nonribosomal peptides activity.
Q48352338	A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein.
Q89928264	A new method for estimating the relative binding free energy, derived from a free energy variational principle for the Pim-1-kinase-ligand and FKBP-ligand systems
Q43181588	A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).
Q51890175	A new paradigm for pattern recognition of drugs.
Q51886827	A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling.
Q70984330	A new procedure for improving the predictiveness of CoMFA models and its application to a set of dihydrofolate reductase inhibitors
Q58225481	A new scaling procedure to correct semiempirical MEP and MEP-derived properties
Q52051313	A new topological index to elucidate apolar hydrocarbons.
Q91943045	A noncanonical binding site of linezolid revealed via molecular dynamics simulations
Q38724984	A novel approach to molecular similarity
Q52075976	A novel method of aligning molecules by local surface shape similarity.
Q59660974	A novel scoring function for molecular docking
Q44536459	A novel view of modelling interactions between synthetic and biological polymers via docking
Q79217779	A novel workflow for the inverse QSPR problem using multiobjective optimization
Q78429542	A pharmacophore model for NK2 antagonist comprising compounds from several structurally diverse classes
Q73331720	A pharmacophore model for dopamine D4 receptor antagonists
Q50616685	A pose prediction approach based on ligand 3D shape similarity.
Q44172742	A practical procedure for the determination of electrostatic charges of large molecules
Q68121886	A prediction of the three-dimensional structure of maize NADP(+)-dependent malate dehydrogenase which explains aspects of light-dependent regulation unique to plant enzymes
Q72933430	A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building
Q41363342	A probabilistic method to report predictions from a human liver microsomes stability QSAR model: a practical tool for drug discovery
Q45059893	A promising enantioselective Diels-Alder dienophile by computer-assisted rational design: 2,5-diphenyl-1-vinyl-borolane
Q68280783	A proposal for the molecular basis of ? and ? opiate receptor differentiation based on modeling of two types of cyclic enkephalins and a narcotic alkaloid
Q57136306	A proposed bioactive conformation of peptide T
Q71699011	A proposed common spatial pharmacophore and the corresponding active conformations of some peptide leukotriene receptor antagonists
Q57138107	A pseudoreceptor docking study of 4,5-?-epoxymorphinans with a range of dielectric constants
Q45768558	A pseudoreceptor modelling study of the varicella-zoster virus and human thymidine kinase binding sites.
Q53118011	A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1.
Q58225433	A quantum-mechanical study of the chain-length dependent stability of the extended and 310-helix conformations in dehydroalanine oligopeptides
Q81581023	A recursive-partitioning model for blood-brain barrier permeation
Q91818380	A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge
Q34186750	A reverse combination of structure-based and ligand-based strategies for virtual screening
Q34937524	A review of protein-small molecule docking methods
Q32058635	A search for sources of drug resistance by the 4D-QSAR analysis of a set of antimalarial dihydrofolate reductase inhibitors
Q44002887	A semiempirical SCF-MO study of the tautomeric forms of 3-acetyl tetronic- and tetramic acids
Q77336352	A semiempirical study on inhibition of catechol O-methyltransferase by substituted catechols
Q43701176	A sequence and structural study of transmembrane helices
Q72816258	A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors
Q30418333	A shape-based machine learning tool for drug design
Q86792219	A simple, fast and convenient new method for predicting the stability of nitro compounds
Q45768209	A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase
Q44882009	A structure-activity relationship study of catechol-O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods
Q44490685	A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase.
Q30355430	A structure-guided approach for protein pocket modeling and affinity prediction.
Q46932252	A successful virtual screening application: prediction of anticonvulsant activity in MES test of widely used pharmaceutical and food preservatives methylparaben and propylparaben
Q52453040	A supermolecule study of the effect of hydration on the conformational behaviour of leucine-enkephalin.
Q47373331	A support vector machine approach to classify human cytochrome P450 3A4 inhibitors
Q43555845	A theoretical approach to the influence of the macrocycle conformation on the molecular electronic structure in Mg-porphyrins
Q40894842	A theoretical model for the Gla-TSR-EGF-1 region of the anticoagulant cofactor protein S: from biostructural pathology to species-specific cofactor activity
Q69601234	A theoretical study of Zn++ interacting with models of ligands present at the thermolysin active site
Q69843553	A theoretical study of angiotensin-converting enzyme inhibitors
Q46699174	A theoretical study of cis-trans isomerisation in H-ZSM5: probing the impact of cluster size and zeolite framework on energetics and structure
Q69601228	A theoretical study of the Si-O bond in disiloxane and related molecules
Q45423719	A three-dimensional model of the human immunodeficiency virus type 1 integration complex
Q44351042	A uniform molecular model of delta opioid agonist and antagonist pharmacophore conformations
Q43773521	A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies
Q52025325	A validation study on the practical use of automated de novo design.
Q33220760	A very large diversity space of synthetically accessible compounds for use with drug design programs
Q48522021	A very short history of structure-based design: how did we get here and where do we need to go?
Q80082286	A virtual active compound produced from the negative image of a ligand-binding pocket, and its application to in-silico drug screening
Q30760210	A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism
Q30847753	A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank.
Q48311186	A well deserved honor: Yvonne Martin, 2009 recipient of the Herman Skolnik Award.
Q55059522	A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils.
Q91406530	A3 adenosine receptor activation mechanisms: molecular dynamics analysis of inactive, active, and fully active states
Q31052629	ADAAPT: Amgen's data access, analysis, and prediction tools
Q42131971	AFAL: a web service for profiling amino acids surrounding ligands in proteins
Q34465525	ALADDIN: an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures
Q51152903	ALOHA: a novel probability fusion approach for scoring multi-parameter drug-likeness during the lead optimization stage of drug discovery.
Q44501183	AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution
Q101210938	AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge
Q73194550	ANLIZE: a molecular mechanics force field visualization tool and its application to 18-crown-6
Q46704259	ANVAS: artificial neural variables adaptation system for descriptor selection
Q92763910	ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths
Q91438193	AZT acts as an anti-influenza nucleotide triphosphate targeting the catalytic site of A/PR/8/34/H1N1 RNA dependent RNA polymerase
Q47742309	Ab initio calculations on iron-porphyrin model systems for intermediates in the oxidative cycle of cytochrome P450s
Q74633115	Ab initio calculations on peptide-derived oxazoles and thiazoles: improved molecular mechanics parameters for the AMBER force field
Q39214506	Ab initio computational modeling of long loops in G-protein coupled receptors
Q73652664	Ab initio study on tautomerism of 2-thiouracil in the gas phase and in solution
Q46531344	Ab initio study on the noncovalent adsorption of camptothecin anticancer drug onto graphene, defect modified graphene and graphene oxide
Q91056192	Absolute and relative pKa predictions via a DFT approach applied to the SAMPL6 blind challenge
Q47567527	Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.
Q57463690	Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field
Q47567557	Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.
Q35209226	Academic librarians at play in the field of cheminformatics: building the case for chemistry research data management
Q64119550	Active learning strategies with COMBINE analysis: new tricks for an old dog
Q83898270	Active site acidic residues and structural analysis of modelled human aromatase: a potential drug target for breast cancer
Q84567874	Active site similarity between human and Plasmodium falciparum phosphodiesterases: considerations for antimalarial drug design
Q72393570	Active-site mobility inhibits reductive dehalogenation of 1,1,1-trichloroethane by cytochrome P450cam
Q61833165	Active-site-directed 3D database searching: Pharmacophore extraction and validation of hits
Q48041442	Activity cliffs in PubChem confirmatory bioassays taking inactive compounds into account
Q61998568	Activity prediction of substrates in NADH-dependent carbonyl reductase by docking requires catalytic constraints and charge parameterization of catalytic zinc environment
Q28611248	Activity, assay and target data curation and quality in the ChEMBL database
Q43060708	Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules.
Q98772845	Addressing free fatty acid receptor 1 (FFAR1) activation using supervised molecular dynamics
Q91624878	Advanced Editorial to announce a JCAMD Special Issue on Artificial Intelligence and Machine Learning
Q94523223	Advances in exploring activity cliffs
Q90797650	Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3 : Binding free energies between flexible ligands and rigid receptors
Q30419602	Alchemical prediction of hydration free energies for SAMPL.
Q74274403	Alignment of flexible molecules at their receptor site using 3D descriptors and Hi-PCA
Q36804259	Alignment-independent technique for 3D QSAR analysis
Q37549101	All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.
Q51080699	AllChem: generating and searching 10(20) synthetically accessible structures.
Q34620088	Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1.
Q38736870	Allosteric modulation model of the mu opioid receptor by herkinorin, a potent not alkaloidal agonist
Q30470433	Alpha shock
Q41264901	An SH2 domain model of STAT5 in complex with phospho-peptides define "STAT5 Binding Signatures".
Q43605227	An ab initio theoretical study of the stereoisomers of tetrahydrocannabinols
Q97427957	An activity prediction model for steroidal and triterpenoidal inhibitors of Acetylcholinesterase enzyme
Q68034483	An approach to computer-aided inhibitor design: application to cathepsin L
Q54451282	An approximate but efficient method to calculate free energy trends by computer simulation: application to dihydrofolate reductase-inhibitor complexes.
Q43463114	An approximation of the Cioslowski–Mixon bond order indexes using the AlteQ approach
Q58043817	An atomistic model of passive membrane permeability: application to a series of FDA approved drugs
Q51536809	An automated PLS search for biologically relevant QSAR descriptors.
Q73604181	An automated method for predicting the positions of hydrogen-bonding atoms in binding sites
Q31004695	An effective simulation of aqueous micellar aggregates by computational models
Q42973032	An efficient synthesis of a rationally designed 1,5 disubstituted imidazole AT(1) angiotensin II receptor antagonist: reorientation of imidazole pharmacophore groups in losartan reserves high receptor affinity and confirms docking studies
Q78057602	An electron-conformational method of identification of pharmacophore and anti-pharmacophore shielding: application to rice blast activity
Q46865357	An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II) from Penicillium purpurogenum.
Q52370106	An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2.
Q57057113	An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge
Q48643849	An exploration of a novel strategy for superposing several flexible molecules.
Q40965375	An extensive ecdysteroid CoMFA.
Q43611751	An improved adaptive genetic algorithm for protein-ligand docking
Q46378945	An improved method to predict the entropy term with the MM/PBSA approach.
Q28210723	An improved nicotinic pharmacophore and a stereoselective CoMFA-model for nicotinic agonists acting at the central nicotinic acetylcholine receptors labelled by
Q36838120	An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
Q51867361	An improved scoring function for suboptimal polar ligand complexes.
Q44343144	An improved theoretical approach to the empirical corrections of density functional theory
Q51967889	An in silico approach for screening flavonoids as P-glycoprotein inhibitors based on a Bayesian-regularized neural network.
Q38559638	An inequality for 3D database searching and its use in evaluating the treatment of conformational flexibility
Q30616554	An informatic pipeline for managing high-throughput screening experiments and analyzing data from stereochemically diverse libraries
Q48110381	An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant
Q35201046	An integrated approach to knowledge-driven structure-based virtual screening
Q54275024	An integrated suite of modeling tools that empower scientists in structure- and property-based drug design.
Q48556761	An interview with Jim Hopkins, CEO of Tripos Discovery Informatics. Interview by Wendy A. Warr.
Q48425108	An interview with Phil Bourne, associate director of the RCSB protein data bank.
Q52561647	An investigation into the construction of molecular models by the template joining method.
Q99366569	An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets
Q35029371	An overview of the diversity represented in commercially-available databases
Q33470339	Analysis and use of fragment-occurrence data in similarity-based virtual screening
Q30332646	Analysis methods for identifying coordinated movements during ligand unbinding.
Q78057597	Analysis of Fas-ligand interactions using a molecular model of the receptor-ligand interface
Q43078853	Analysis of SM8 and Zap TK calculations and their geometric sensitivity
Q51070510	Analysis of stacking overlap in nucleic acid structures: algorithm and application.
Q46947386	Analysis of the activation mechanism of the guinea-pig Histamine H1-receptor
Q45901560	Annular tautomerism: experimental observations and quantum mechanics calculations.
Q48113143	Antagonist-perturbation mechanism for activation function-2 fixed motifs: active conformation and docking mode of retinoid X receptor antagonists
Q91596914	Anti-malarial, cytotoxicity and molecular docking studies of quinolinyl chalcones as potential anti-malarial agent
Q72933435	Antifungal triazole alcohols: a comparative analysis of structure-activity, structure-teratogenicity and structure-therapeutic index relationships using the Multiple Computer-Automated Structure Evaluation (Multi-CASE) methodology
Q44087620	Antimalarial activity of synthetic 1,2,4-trioxanes and cyclic peroxy ketals, a quantum similarity study
Q44319409	Antioxidant properties of phenolic Schiff bases: structure-activity relationship and mechanism of action.
Q37368872	Antitumor agents 252. Application of validated QSAR models to database mining: discovery of novel tylophorine derivatives as potential anticancer agents
Q86310322	App-etite for change
Q91538152	Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies
Q41515537	Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition
Q51939686	Application of artificial neural networks and DFT-based parameters for prediction of reaction kinetics of ethylbenzene dehydrogenase.
Q30585010	Application of multivariate data analysis methods to comparative molecular field analysis (CoMFA) data: proton affinities and pKa prediction for nucleic acids components
Q68049865	Application of semi-empirical and ab initio quantum mechanical calculations
Q54580789	Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors.
Q100694740	Application of target repositioning and in silico screening to exploit fatty acid binding proteins (FABPs) from Echinococcus multilocularis as possible drug targets
Q90865437	Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent
Q70790876	Applications of momentum-space similarity
Q43883717	Applications of rule-induction in the derivation of quantitative structure-activity relationships
Q51023570	Applying forces to elastic network models of large biomolecules using a haptic feedback device.
Q44178393	Approaching the 5-HT₃ receptor heterogeneity by computational studies of the transmembrane and intracellular domains
Q83199715	Are predefined decoy sets of ligand poses able to quantify scoring function accuracy?
Q95938036	Artificial intelligence in chemistry and drug design
Q33519580	Artificial neural network study on organ-targeting peptides
Q47922804	As-Rigid-As-Possible molecular interpolation paths
Q46720946	Asp746 to glycine change may have a greater influence than Cys751 to serine change in accounting for ligand selectivity between EGFR and HER-2 at the ATP site
Q46321399	Aspects of the mechanism of catalysis of glucose oxidase: a docking, molecular mechanics and quantum chemical study
Q90442960	Assessing and improving the performance of consensus docking strategies using the DockBox package
Q48113134	Assessing protein-ligand binding modes with computational tools: the case of PDE4B.
Q89928274	Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge
Q53423422	Assessing the lipophilicity of fragments and early hits.
Q91917408	Assessing the performance of three resveratrol in binding with SIRT1 by molecular dynamics simulation and MM/GBSA methods: the weakest binding of resveratrol 3 to SIRT1 triggers a possibility of dissociation from its binding site
Q55037679	Assessing the stability of free-energy perturbation calculations by performing variations in the method.
Q47696423	Assessment of tautomer distribution using the condensed reaction graph approach.
Q86295911	Assessment of the tautomeric population of benzimidazole derivatives in solution: a simple and versatile theoretical-experimental approach
Q47698531	Assessment of uncertainty in chemical models by Bayesian probabilities: Why, when, how?
Q46703807	Association of cytochrome P450 enzymes is a determining factor in their catalytic activity
Q31044283	Association of transmembrane helices: what determines assembling of a dimer?
Q31147673	AstexViewer: a visualisation aid for structure-based drug design
Q34338177	AtlasCBS: a web server to map and explore chemico-biological space.
Q89691238	Atomistic computer simulations on multi-loaded PAMAM dendrimers: a comparison of amine- and hydroxyl-terminated dendrimers
Q92720683	Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts
Q38782136	Atomistic lattice simulation of high Tc oxides
Q39354173	Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign
Q82277218	Automated QSPR through Competitive Workflow
Q33797738	Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design.
Q47921236	Automated computational screening of the thiol reactivity of substituted alkenes.
Q52473270	Automated conformational analysis: algorithms for the efficient construction of low-energy conformations.
Q57966457	Automated docking and molecular dynamics simulations of nimesulide in the cyclooxygenase active site of human prostaglandin-endoperoxide synthase-2 (COX-2)
Q78057582	Automated docking of 82 N-benzylpiperidine derivatives to mouse acetylcholinesterase and comparative molecular field analysis with 'natural' alignment
Q57976077	Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling
Q52376640	Automated molecular design: a new fragment-joining algorithm.
Q44823868	Automated molecule editing in molecular design
Q67558783	Automated site-directed drug design: an assessment of the transferability of atomic residual charges (CNDO) for molecular fragments
Q52482964	Automated site-directed drug design: approaches to the formation of 3D molecular graphs.
Q67558781	Automated site-directed drug design: searches of the Cambridge Structural Database for bond lengths in molecular fragments to be used for automated structure assembly
Q67558780	Automated site-directed drug design: the generation of a basic set of fragments to be used for automated structure assembly
Q45964726	Automatic QSAR modeling of ADME properties: blood-brain barrier penetration and aqueous solubility.
Q52482973	Automatic log P estimation based on combined additive modeling methods.
Q68274966	Automatic search for maximum similarity between molecular electrostatic potential distributions
Q67976698	Automatic superposition of drug molecules based on their common receptor site
Q35803775	Avalanche for shape and feature-based virtual screening with 3D alignment.
Q36109714	Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules
Q28296578	BALLView: an object-oriented molecular visualization and modeling framework
Q92899539	BCL::Mol2D-a robust atom environment descriptor for QSAR modeling and lead optimization
Q36801376	BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.
Q51979864	BODIL: a molecular modeling environment for structure-function analysis and drug design.
Q90865429	BRADSHAW: a system for automated molecular design
Q33251138	BRUTUS: optimization of a grid-based similarity function for rigid-body molecular superposition. II. Description and characterization
Q46836531	BUILDER v.2: improving the chemistry of a de novo design strategy
Q47742352	BUNDLE: a program for building the transmembrane domains of G-protein-coupled receptors
Q33260987	Balancing focused combinatorial libraries based on multiple GPCR ligands
Q36303825	Bayesian molecular design with a chemical language model.
Q98184691	Benchmarking GPCR homology model template selection in combination with de novo loop generation
Q112570463	Benchmarking ensemble docking methods in D3R Grand Challenge 4
Q98772844	Benchmarking the performance of MM/PBSA in virtual screening enrichment using the GPCR-Bench dataset
Q30620538	Benefits of statistical molecular design, covariance analysis, and reference models in QSAR: a case study on acetylcholinesterase
Q44711416	Benzimidazole derivatives. 4. The recognition of the voluminous substituent attached to the basic amino group of 5-HT4 receptor antagonists
Q114863710	Best practices for repurposing studies
Q42639520	Bias, reporting, and sharing: computational evaluations of docking methods
Q53076305	Biased retrieval of chemical series in receptor-based virtual screening.
Q28654673	Bigger data, collaborative tools and the future of predictive drug discovery
Q56975687	Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods
Q48023567	Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.
Q38302840	Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations.
Q114226105	Binding free energies for the SAMPL8 CB8 “Drugs of Abuse” challenge from umbrella sampling combined with Hamiltonian replica exchange
Q37588656	Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).
Q91376128	Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods
Q59539663	Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase
Q47827032	Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2.
Q48057664	Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR.
Q50622600	Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A2A receptor.
Q44490732	Binding models of reversible inhibitors to type-B monoamine oxidase
Q44667605	Binding of alpha-hydroxy-beta-amino acid inhibitors to methionine aminopeptidase. The performance of two types of scoring functions
Q41521138	Binding of carboxylate and trimethylammonium salts to octa-acid and TEMOA deep-cavity cavitands
Q33599960	Binding of cyclic carboxylates to octa-acid deep-cavity cavitand
Q85037178	Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations
Q54413507	Binding of the Zn2+ ion to ferric uptake regulation protein from E. coli and the competition with Fe2+ binding: a molecular modeling study of the effect on DNA binding and conformational changes of Fur.
Q47659739	Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method
Q37363075	Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations
Q72069925	Bioactive design: forward to new frontiers
Q47391842	Bioactive focus in conformational ensembles: a pluralistic approach
Q48012449	Biologically relevant conformational features of linear and cyclic proteolipid protein (PLP) peptide analogues obtained by high-resolution nuclear magnetic resonance and molecular dynamics.
Q51277956	Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity.
Q90101459	Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?
Q33601586	Biophysical approaches to G protein-coupled receptors: structure, function and dynamics
Q33928781	Biosensor-based small molecule fragment screening with biolayer interferometry.
Q26864619	Blind prediction of HIV integrase binding from the SAMPL4 challenge
Q40579705	Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method
Q34541312	Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge
Q48054550	Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections
Q34257034	Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.
Q34409381	Blind prediction of solvation free energies from the SAMPL4 challenge.
Q57829052	Blind prediction test of free energies of hydration with COSMO-RS
Q91396118	Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations
Q38597033	Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations.
Q90295745	Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4
Q28818251	Blinded predictions of distribution coefficients in the SAMPL5 challenge
Q39509919	Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge
Q91216246	Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge
Q31146521	Blowing a breath of fresh share on data
Q40775428	Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
Q56985169	Bond-based 2D TOMOCOMD-CARDD approach for drug discovery: aiding decision-making in ‘in silico’ selection of new lead tyrosinase inhibitors
Q56985185	Bond-based global and local (bond, group and bond-type) quadratic indices and their applications to computer-aided molecular design. 1. QSPR studies of diverse sets of organic chemicals
Q33335184	Bond-based linear indices in QSAR: computational discovery of novel anti-trichomonal compounds.
Q58114855	Boosted feature selectors: a case study on prediction P-gp inhibitors and substrates
Q47622421	Boosted leave-many-out cross-validation: the effect of training and test set diversity on PLS statistics
Q47577468	Box size effects are negligible for solvation free energies of neutral solutes
Q52427344	Brownian dynamics simulation of protein association.
Q30844883	C-QSAR: a database of 18,000 QSARs and associated biological and physical data
Q38772488	CADD medicine: design is the potion that can cure my disease
Q33350494	CAL3JHH: a Java program to calculate the vicinal coupling constants (3J H,H) of organic molecules
Q73604209	CAMDAS: an automated conformational analysis system using molecular dynamics. Conformational Analyzer with Molecular Dynamics And Sampling
Q46602190	CAVEAT: a program to facilitate the design of organic molecules
Q46022295	CCDC well groomed: an interview with Colin Groom, Executive Director, Cambridge Crystallographic Data Centre, and Frank Allen, Emeritus Fellow.
Q47694932	CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2.
Q68559277	CGEMA and VGAP: a Colour Graphics Editor for Multiple Alignment using a variable GAP penalty. Application to the muscarinic acetylcholine receptor
Q33350276	CONFIRM: connecting fragments found in receptor molecules
Q71851446	CORCEMA evaluation of the potential role of intermolecular transferred NOESY in the characterization of ligand-receptor complexes
Q67822568	COSMIC(90): An improved molecular mechanics treatment of hydrocarbons and conjugated systems
Q91480962	COSMO-RS based predictions for the SAMPL6 logP challenge
Q48882491	COSMO-RS: a novel view to physiological solvation and partition questions.
Q51924209	Caco-2 cell permeability modelling: a neural network coupled genetic algorithm approach.
Q91459326	Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3
Q57397675	Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge
Q51901592	Calculating physical properties of organic compounds for environmental modeling from molecular structure.
Q30668824	Calculating the knowledge-based similarity of functional groups using crystallographic data
Q36120306	Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas
Q70790866	Calculation of hydrophobic parameters directly from three-dimensional structures using comparative molecular field analysis
Q71483770	Calculation of solvation and binding free energy differences between VX-478 and its analogs by free energy perturbation and AMSOL methods
Q51914537	Calculations of protein-ligand binding entropy of relative and overall molecular motions.
Q41958908	Calibrative approaches to protein solubility modeling of a mutant series using physicochemical descriptors
Q51311642	Call for Papers: GRC, CADD, and statistics, and all that.
Q94466096	Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein
Q51309798	Can topological indices transmit information on properties but not on structures?
Q82908096	Can we really do computer-aided drug design?
Q52942162	Can we separate active from inactive conformations?
Q80467476	Can we use docking and scoring for hit-to-lead optimization?
Q57357387	Cannabinoid CB1 receptor recognition of endocannabinoids via the lipid bilayer: molecular dynamics simulations of CB1 transmembrane helix 6 and anandamide in a phospholipid bilayer
Q44064526	Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites
Q45092503	Cardio-vascular safety beyond hERG: in silico modelling of a guinea pig right atrium assay
Q41872137	Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction
Q80865396	Categorical QSAR models for skin sensitization based on local lymph node assay measures and both ground and excited state 4D-fingerprint descriptors
Q52467410	Cavity search: an algorithm for the isolation and display of cavity-like binding regions.
Q33384498	ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr
Q78752864	Chain melting temperature estimation for phosphatidyl cholines by quantum mechanically derived quantitative structure property relationships
Q82324123	Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes
Q84143317	Challenges of fragment screening
Q46627471	Challenging the gold standard for 3D-QSAR: template CoMFA versus X-ray alignment
Q36794966	Characterising the geometric diversity of functional groups in chemical databases
Q90416615	Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach
Q85028582	Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses
Q46630848	Characterization of beta3-adrenergic receptor: determination of pharmacophore and 3D QSAR model for beta3 adrenergic receptor agonism.
Q45902527	Characterization of dipeptidylcarboxypeptidase of Leishmania donovani: a molecular model for structure based design of antileishmanials.
Q57138096	Characterization of low-energy conformational domains for Met-enkephalin
Q69724842	Charge calculations in molecular mechanics 7: application to polar pi systems incorporating nitro, cyano, amino, C=S and thio substituents
Q68034485	Charge calculations in molecular mechanics. IX. A general parameterisation of the scheme for saturated halogen, oxygen and nitrogen compounds
Q70232998	Charge calculations in molecular mechanics. Part 8. Partial atomic charges from classical calculations
Q34019261	Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models
Q74505235	Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field MAB
Q44109237	Charge-transfer interactions in the inhibition of MAO-A by phenylisopropylamines--a QSAR study.
Q33392980	ChemGPS-NP(Web): chemical space navigation online
Q44202556	ChemStable: a web server for rule-embedded naïve Bayesian learning approach to predict compound stability
Q35453774	Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes
Q51079623	Chemical space networks: a powerful new paradigm for the description of chemical space.
Q51703673	Chemical space sampling by different scoring functions and crystal structures.
Q34380828	Cheminformatics aspects of high throughput screening: from robots to models: symposium summary
Q90433622	Chemistry, information and Frank: a tribute to Frank Brown
Q30875895	Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries
Q52373578	Chemometric QSAR studies of antifungal azoxy compounds.
Q53914324	Chemometric rationalization of the structural and physicochemical basis for selective cyclooxygenase-2 inhibition: toward more specific ligands.
Q70661457	Chiral chromatography and multivariate quantitative structure-property relationships of benzimidazole sulphoxides
Q57250693	Class IV charge models: A new semiempirical approach in quantum chemistry
Q73013892	Classical QSAR and comparative molecular field analyses of the host-guest interaction of organic molecules with cyclodextrins
Q47622495	Classification of HIV protease inhibitors on the basis of their antiviral potency using radial basis function neural networks
Q30983472	Classification of a large anticancer data set by adaptive fuzzy partition
Q74505239	Classification of auxin plant hormones by interaction property similarity indices
Q52061314	Classification of protein disulphide-bridge topologies.
Q30952694	Classification scheme for the design of serine protease targeted compound libraries
Q50181313	ClogP(alk): a method for predicting alkane/water partition coefficient.
Q44670603	Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation
Q33449492	Closing the side-chain gap in protein loop modeling
Q47717539	Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding.
Q31033965	CoMFA and CoMSIA 3D-quantitative structure-activity relationship model on benzodiazepine derivatives, inhibitors of phosphodiesterase IV.
Q44667595	CoMFA and docking study of novel estrogen receptor subtype selective ligands
Q52545360	CoMFA validation of the superposition of six classes of compounds which block GABA receptors non-competitively.
Q32058642	CoMFA-based comparison of two models of binding site on adenosine A1 receptor.
Q48006451	Collaborating to improve the use of free-energy and other quantitative methods in drug discovery.
Q48455544	Collaboration, competition, validation and plans for the future : an interview with Gerard Kleywegt, Head of the Protein Data Bank in Europe. Interviewed by Wendy A Warr.
Q31939358	CombiDOCK: structure-based combinatorial docking and library design
Q30628860	Combinatorial docking and combinatorial chemistry: design of potent non-peptide thrombin inhibitors
Q33481042	Combinatorial library-based design with Basis Products
Q33548819	Combinatorial-computational-chemoinformatics (C3) approach to finding and analyzing low-energy tautomers.
Q43724449	Combined QSAR and molecule docking studies on predicting P-glycoprotein inhibitors
Q100949808	Combined experimental and quantum mechanical elucidation of the synthetically accessible stereoisomers of Hydroxyestradienone (HED), the starting material for vilaprisan synthesis
Q39489949	Combined use of pharmacophoric models together with drug metabolism and genotoxicity "in silico" studies in the hit finding process.
Q38993439	Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection
Q30778906	Combining NMR spectral and structural data to form models of polychlorinated dibenzodioxins, dibenzofurans, and biphenyls binding to the AhR.
Q84615371	Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules
Q40959163	Combining docking-based comparative intermolecular contacts analysis and k-nearest neighbor correlation for the discovery of new check point kinase 1 inhibitors
Q100505466	Combining fragment docking with graph theory to improve ligand docking for homology model structures
Q47809580	Combining fragment homology modeling with molecular dynamics aims at prediction of Ca²⁺ binding sites in CaBPs
Q42242201	Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4.
Q51410824	Combining molecular dynamics simulation and ligand-receptor contacts analysis as a new approach for pharmacophore modeling: beta-secretase 1 and check point kinase 1 as case studies.
Q38608749	Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2.
Q44225818	Common prevalence of alanine and glycine in mobile reactive centre loops of serpins and viral fusion peptides: do prions possess a fusion peptide?
Q28268675	Community benchmarks for virtual screening
Q79660689	Comparative QSAR studies on PAMPA/modified PAMPA for high throughput profiling of drug absorption potential with respect to Caco-2 cells and human intestinal absorption
Q79356133	Comparative and pharmacophore model for deacetylase SIRT1
Q57966471	Comparative binding energy analysis
Q40547496	Comparative binding energy analysis of haloalkane dehalogenase substrates: modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations.
Q67865141	Comparative conformational analysis of [D-Pen2,D-Pen5]enkephalin (DPDPE): a molecular mechanics study
Q71699017	Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4
Q45391940	Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of thiazolone derivatives as hepatitis C virus NS5B polymerase allosteric inhibitors
Q52067622	Comparative molecular field analysis (coMFA) study of epothilones-tubulin depolymerization inhibitors: pharmacophore development using 3D QSAR methods.
Q77365335	Comparative molecular field analysis and energy interaction studies of thrombin-inhibitor complexes
Q73315113	Comparative molecular field analysis and molecular modeling studies of 20-(S)-camptothecin analogs as inhibitors of DNA topoisomerase I and anticancer/antitumor agents
Q45046460	Comparative molecular field analysis of CCK-A antagonists using field-fit as an alignment technique. A convenient guide to design new CCK-A ligands
Q77428769	Comparative molecular field analysis of artemisinin derivatives: ab initio versus semiempirical optimized structures
Q71483792	Comparative molecular field analysis of non-steroidal aromatase inhibitors related to fadrozole
Q56622993	Comparative molecular modelling study of the calcium channel blockers nifedipine and black mamba toxin FS2
Q30656455	Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries
Q74274396	Comparative receptor mapping of serotoninergic 5-HT3 and 5-HT4 binding sites
Q79158020	Comparative residue interaction analysis (CoRIA): a 3D-QSAR approach to explore the binding contributions of active site residues with ligands
Q39545851	Comparative review of molecular modelling software for personal computers
Q33201269	Comparative study of several algorithms for flexible ligand docking
Q79846741	Comparative study of the prereactive protein kinase A Michaelis complex with kemptide substrate
Q33515060	Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists
Q47631131	Comparing pharmacophore models derived from crystallography and NMR ensembles
Q53075202	Comparing the performance of meta-classifiers-a case study on selected imbalanced data sets relevant for prediction of liver toxicity.
Q74835547	Comparison of 3D quantitative structure-activity relationship methods: analysis of the in vitro antimalarial activity of 154 artemisinin analogues by hypothetical active-site lattice and comparative molecular field analysis
Q52650065	Comparison of a 3D-model of the classical alpha-scorpion toxin V from Leiurus quinquestriatus quinquestriatus with other scorpion toxins.
Q79750135	Comparison of a homology model and the crystallographic structure of human 11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1) in a structure-based identification of inhibitors
Q91135908	Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4
Q77365338	Comparison of azacyclic urea A-98881 as HIV-1 protease inhibitor with cage dimeric N-benzyl 4-(4-methoxyphenyl)-1,4-dihydropyridine as representative of a novel class of HIV-1 protease inhibitors: a molecular modeling study
Q85323813	Comparison of bioactive chemical space networks generated using substructure- and fingerprint-based measures of molecular similarity
Q81437638	Comparison of commercially available genetic algorithms: gas as variable selection tool
Q64112563	Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques
Q51999968	Comparison of correlation vector methods for ligand-based similarity searching.
Q44343648	Comparison of cyclic delta-opioid peptides with non-peptide delta-agonist spiroindanyloxymorphone (SIOM) using the message-address concept: a molecular modeling study
Q40867870	Comparison of protein surfaces using a genetic algorithm
Q39909719	Comparison of structure fingerprint and molecular interaction field based methods in explaining biological similarity of small molecules in cell-based screens
Q64111812	Comparison of substructural epitopes in enzyme active sites using self-organizing maps
Q70280723	Comparison of the X-ray structure of baboon alpha-lactalbumin and the tertiary predicted computer models of human alpha-lactalbumin
Q57463686	Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges
Q35168275	Comparison of three GPCR structural templates for modeling of the P2Y12 nucleotide receptor
Q52220779	Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors.
Q39248121	Compilation and physicochemical classification analysis of a diverse hERG inhibition database
Q64900233	Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen.
Q43853536	Composite multi-parameter ranking of real and virtual compounds for design of MC4R agonists: renaissance of the Free-Wilson methodology
Q54494731	Comprehensive model of wild-type and mutant HIV-1 reverse transciptases.
Q51615421	Computation of 3D queries for ROCS based virtual screens.
Q47742338	Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases
Q39551290	Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.
Q51655176	Computation space.
Q51604799	Computation, experiment and molecular design.
Q39743323	Computational analysis of EBNA1 "druggability" suggests novel insights for Epstein-Barr virus inhibitor design
Q70984340	Computational analysis of binding affinity and neural response at the L-alanine receptor
Q30562222	Computational analysis of local membrane properties
Q35589799	Computational and biophysical approaches to protein-protein interaction inhibition of Plasmodium falciparum AMA1/RON2 complex.
Q36104862	Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1.
Q38829916	Computational approaches for predicting mutant protein stability
Q50973091	Computational assessment of synthetic procedures.
Q53608885	Computational atomistic blueprinting of novel conducting copolymers using particle swarm optimization.
Q39676642	Computational chemistry and cheminformatics: an essay on the future
Q89020557	Computational chemistry at Janssen
Q46294568	Computational chemistry in 25 years
Q39686921	Computational chemistry in pharmaceutical research: at the crossroads
Q30361816	Computational chemogenomics: is it more than inductive transfer?
Q52418847	Computational combinatorial ligand design: application to human alpha-thrombin.
Q52083095	Computational design of D-peptide inhibitors of hepatitis delta antigen dimerization.
Q43016539	Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics.
Q47778490	Computational design of bio-inspired carnosine-based HOBr antioxidants
Q91624909	Computational design, synthesis and evaluation of new sulphonamide derivatives targeting HIV-1 gp120
Q47957502	Computational discovery of putative quorum sensing inhibitors against LasR and RhlR receptor proteins of Pseudomonas aeruginosa
Q38299764	Computational docking simulations of a DNA-aptamer for argininamide and related ligands.
Q96128888	Computational exploration and experimental validation to identify a dual inhibitor of cholinesterase and amyloid-beta for the treatment of Alzheimer's disease
Q33469692	Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site
Q34127928	Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge
Q33408994	Computational identification of epitopes in the glycoproteins of novel bunyavirus (SFTS virus) recognized by a human monoclonal antibody (MAb 4-5).
Q40212184	Computational insights into the interaction mechanism of triazolyl substituted tetrahydrobenzofuran derivatives with H(+),K(+)-ATPase at different pH.
Q90474289	Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulators
Q39506214	Computational insights into the selectivity mechanism of APP-IP over matrix metalloproteinases
Q84711500	Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17β-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps
Q90814692	Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies
Q33886274	Computational methods for the structural alignment of molecules
Q34126654	Computational model of the complex between GR113808 and the 5-HT4 receptor guided by site-directed mutagenesis and the crystal structure of rhodopsin
Q47442677	Computational modeling and in-vitro/in-silico correlation of phospholipid-based prodrugs for targeted drug delivery in inflammatory bowel disease.
Q79883949	Computational models to predict blood-brain barrier permeation and CNS activity
Q36624603	Computational photochemistry of retinal proteins
Q42107457	Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds
Q44245923	Computational prediction of kink properties of helices in membrane proteins.
Q36297180	Computational simulations of the conformational behaviour of the adhesive proteins RGDS fragment
Q46703802	Computational studies and drug design for HIV-1 reverse transcriptase inhibitors of 3',4'-di-O-(S)-camphanoyl-(+)-cis-khellactone (DCK) analogs
Q47972915	Computational studies of new potential antimalarial compounds--stereoelectronic complementarity with the receptor
Q33560786	Computational studies on the interaction of ABO-active saccharides with the norovirus VA387 capsid protein can explain experimental binding data
Q43734813	Computational study of elements of stability of a four-helix bundle protein biosurfactant.
Q31080420	Computational study of pH-dependent oligomerization and ligand binding in Alt a 1, a highly allergenic protein with a unique fold
Q44167541	Computational study of the catalytic domain of human neutrophil collagenase. specific role of the S3 and S'3 subsites in the interaction with a phosphonate inhibitor.
Q85651591	Computational study of the effects of protein tyrosine nitrations on the catalytic activity of human thymidylate synthase
Q51823568	Computational study of the heterodimerization between mu and delta receptors.
Q37503295	Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore
Q38296034	Computational study on mechanism of G-quartet oligonucleotide T40214 selectively targeting Stat3.
Q45250354	Computational study on the molecular inclusion of andrographolide by cyclodextrin.
Q52482980	Computer Automated Structure Evaluation (CASE) of the teratogenicity of retinoids with the aid of a novel geometry index.
Q43704069	Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors
Q68846659	Computer graphic study on models of the molybdenum cofactor of xanthine oxidase
Q41212308	Computer modelling: future directions
Q30360045	Computer simulation of biological interactions and reactivity.
Q38782190	Computer simulation of liquid crystals
Q38359548	Computer simulation of the binding of amonafide and azonafide to DNA.
Q42210671	Computer simulation of the binding of quinocarcin to DNA. Prediction of mode of action and absolute configuration
Q69601244	Computer simulation of the conformational behavior of cholecystokinin fragments: conformational families of sulfated CCK8
Q68121898	Computer simulation of the conformational behaviour of angiotensinogen (6-13) renin substrate
Q43490687	Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus
Q69844592	Computer simulations in zeolite chemistry
Q45105290	Computer-aided active-site-directed modeling of the herpes simplex virus 1 and human thymidine kinase
Q74097068	Computer-aided design and activity prediction of leucine aminopeptidase inhibitors
Q51393402	Computer-aided design of novel antibacterial 3-hydroxypyridine-4-ones: application of QSAR methods based on the MOLMAP approach.
Q48344517	Computer-aided drug design at Boehringer Ingelheim.
Q82324131	Computer-aided drug design platform using PyMOL
Q72741860	Computer-aided drug design: a free energy perturbation study on the binding of methyl-substituted pterins and N5-deazapterins to dihydrofolate reductase
Q28256647	Computer-aided drug design: the next 20 years
Q57074609	Computer-aided drug discovery and design
Q36179855	Computer-aided drug discovery research at a global contract research organization
Q50506096	Computer-aided molecular design under the SWOTlight.
Q68121893	Computer-aided molecular modeling and design of DNA-inserting molecules
Q41448933	Computer-aided molecular modeling of a D2-agonist dopamine pharmacophore.
Q41265612	Computer-aided molecular modelling: research study or research tool?
Q34348773	Computer-aided structure-affinity relationships in a set of piperazine and 3,8-diazabicyclo[3.2.1]octane derivatives binding to the mu-opioid receptor
Q33748641	Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase.
Q84562022	Computer-assisted study on the reaction between pyruvate and ylide in the pathway leading to lactyl-ThDP
Q24289469	Confidence limits, error bars and method comparison in molecular modeling. Part 1: the calculation of confidence intervals
Q39116494	Confidence limits, error bars and method comparison in molecular modeling. Part 2: comparing methods
Q67941473	Conformation of receptor-associated PGI2: an investigation by molecular modeling
Q34560835	Conformation-activity relationships of opiate analgesics
Q68171365	Conformational analyses on histamine H2-receptor antagonists
Q47742296	Conformational analysis of [Met5]-enkephalin: solvation and ionization considerations
Q57135526	Conformational analysis of a farnesyltransferase peptide inhibitor, CVIM
Q43805835	Conformational analysis of kainate in aqueous solution in relation to its binding to AMPA and kainic acid receptors
Q92829689	Conformational analysis of macrocycles: comparing general and specialized methods
Q46467177	Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods
Q43979142	Conformational analysis of nevirapine, a non-nucleoside HIV-1 reverse transcriptase inhibitor, based on quantum mechanical calculations
Q62648702	Conformational analysis of six- and twelve-membered ring compounds by molecular dynamics
Q84904047	Conformational analysis of the ΜΒΡ83-99 (Phe91) and ΜΒΡ83-99 (Tyr91) peptide analogues and study of their interactions with the HLA-DR2 and human TCR receptors by using molecular dynamics
Q38350507	Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4: implications for design of non-hydrolysable mimetics
Q68012967	Conformational analysis. Part 16. Conformational free energies in substituted piperidines and piperidinium salts
Q52549169	Conformational and receptor-binding properties of the insect neuropeptide proctolin and its analogues.
Q52417441	Conformational behaviour and molecular similarity of some beta 1-adrenergic ligands
Q70984336	Conformational behaviour of the antineoplastic peptide dolastatin-10 and of two mutated derivatives
Q52351880	Conformational energy downward driver (CEDD): characterization and calibration of the method.
Q57136198	Conformational energy penalties of protein-bound ligands
Q89484077	Conformational ensemble comparison for small molecules in drug discovery
Q40116297	Conformational flexibility of DENV NS2B/NS3pro: from the inhibitor effect to the serotype influence.
Q43120311	Conformational landscape of platinum(II)-tetraamine complexes: DFT and NBO studies
Q33893624	Conformational preferences of the potent dopamine reuptake blocker BTCP and its analogs and their incorporation into a pharmacophore model
Q60459611	Conformational properties of amphotericin B amide derivatives--impact on selective toxicity
Q52542613	Conformational properties of pyrethroids.
Q52422829	Conformational search by potential energy annealing: algorithm and application to cyclosporin A.
Q48083247	Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis
Q57594206	Conformational studies of immunodominant myelin basic protein 1–11 analogues using NMR and molecular modeling
Q41116526	Conformational studies on (+)-anatoxin-a and derivatives
Q46924588	Conformational studies on the four stereoisomers of the novel anticholinergic 4-(dimethylamino)-2-phenyl-2-(2-pyridyl)pentanamide
Q43566216	Conformational study of insect adipokinetic hormones using NMR constrained molecular dynamics
Q61326962	Conformational variety for the ansa chain of rifamycins: comparison of observed crystal structures and molecular dynamics simulations
Q52401179	Conformations of large cycloalkanes: cyclooctadecane, cyclononadecane and cycloicosane.
Q47571750	Congestion game scheduling for virtual drug screening optimization.
Q34440071	Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors
Q33530647	Consensus model for identification of novel PI3K inhibitors in large chemical library
Q46916180	Conserved network properties of helical membrane protein structures and its implication for improving membrane protein homology modeling at the twilight zone
Q37198661	Considerations and recent advances in QSAR models for cytochrome P450-mediated drug metabolism prediction
Q52398725	Constitutional, configurational and conformational analysis of transition metal coordination complexes.
Q69601237	Constrained search of conformational hyperspace
Q42609883	Construction of 3D models of the CYP11B family as a tool to predict ligand binding characteristics
Q46758096	Construction of 4D-QSAR models for use in the design of novel p38-MAPK inhibitors
Q73331705	Construction of a full three-dimensional model of the transpeptidase domain of Streptococcus pneumoniae PBP2x starting from its Calpha-atom coordinates
Q56982829	Continuous indicator fields: a novel universal type of molecular fields
Q30457582	Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations
Q45945644	Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization.
Q89543575	Convolutional neural network scoring and minimization in the D3R 2017 community challenge
Q91135888	Correction to: BRADSHAW: a system for automated molecular design
Q58558877	Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A adenosine receptor orthosteric binding site using a molecular docking approach? Insights from Dockbench
Q45216911	Count on kappa
Q52382633	Coupling constants again: experimental restraints in structure refinement.
Q91264661	Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4
Q57794478	Covalent docking of selected boron-based serine beta-lactamase inhibitors
Q100440524	Covalent inhibitor reactivity prediction by the electrophilicity index-in and out of scope
Q35230342	Creating and virtually screening databases of fluorescently-labelled compounds for the discovery of target-specific molecular probes.
Q114226104	Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations
Q35201628	Crystal structure of an antiviral ankyrin targeting the HIV-1 capsid and molecular modeling of the ankyrin-capsid complex
Q39621578	Crystallographic modelling
Q69500307	Crystallographic studies and semi-empirical MNDO calculations on quisqualic acid and its analogues: systems containing unusual pyramidal heterocyclic ring nitrogens
Q40565305	Current methods for site-directed structure generation.
Q57966454	Current perspective of information technologies in drug discovery
Q57017035	Current trends in lead discovery: are we looking for the appropriate properties?
Q42746608	Customizing scoring functions for docking
Q33593269	Cyclodextrin KnowledgeBase a web-based service managing CD-ligand complexation data
Q73803107	Cyclophosphamides as hypoxia-activated diffusible cytotoxins: a theoretical study
Q46050747	D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies
Q64118692	D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings
Q91538145	D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors
Q91135912	D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU
Q39328873	D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions
Q92892915	D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies
Q72240654	DBMAKER: a set of programs to generate three-dimensional databases based upon user-specified criteria
Q83012465	DFT calculation of four new potential agents muscarinic of bispyridinium type: structure, synthesis, biological activity, hydration, and relations with the potents W84 and DUO-3O
Q39869132	DFT-based QSAR and QSPR models of several cis-platinum complexes: solvent effect
Q33843997	DFT-based prediction of reactivity of short-chain alcohol dehydrogenase.
Q27231136	DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
Q92260441	DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information
Q52567958	DR2DI: a powerful computational tool for predicting novel drug-disease associations.
Q30770159	DREAM++: flexible docking program for virtual combinatorial libraries
Q46937054	Darwinian docking
Q36852271	Data modelling with neural networks: advantages and limitations.
Q30970805	Data quality in drug discovery: the role of analytical performance in ligand binding assays
Q42684716	Data sharing as an issue
Q30735723	Data sharing matters
Q91624891	Data structures for computational compound promiscuity analysis and exemplary applications to inhibitors of the human kinome
Q30837195	DataCite and DOI names for research data
Q73913472	Database diversity assessment: new ideas, concepts, and tools
Q30194891	De novo and inverse folding predictions of protein structure and dynamics
Q80541220	De novo design and synthetic accessibility
Q51531786	De novo design by pharmacophore-based searches in fragment spaces.
Q30885899	De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
Q54452978	De novo ligand design with explicit water molecules: an application to bacterial neuraminidase.
Q38305525	Deciphering common failures in molecular docking of ligand-protein complexes.
Q91732591	Deciphering structure, function and mechanism of Plasmodium IspD homologs from their evolutionary imprints
Q92507759	Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4
Q100440522	DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology
Q51658614	Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions.
Q79177476	Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling
Q34078930	DemQSAR: predicting human volume of distribution and clearance of drugs
Q83150153	Democratization of computational chemistry and chem(o)informatics
Q89450854	Demystifying the pH dependent conformational changes of human heparanase pertaining to structure-function relationships: an in silico approach
Q43606860	Density functional and molecular docking studies towards investigating the role of single-wall carbon nanotubes as nanocarrier for loading and delivery of pyrazinamide antitubercular drug onto pncA protein.
Q57905894	Dependency of ligand free energy landscapes on charge parameters and solvent models
Q72593895	Derivation of a 3D pharmacophore model for the angiotensin-II site one receptor
Q30576048	Derivatives in discrete mathematics: a novel graph-theoretical invariant for generating new 2/3D molecular descriptors. I. Theory and QSPR application
Q51311524	Descriptor collision and confusion: toward the design of descriptors to mask chemical structures.
Q31149833	Descriptors you can count on? Normalized and filtered pharmacophore descriptors for virtual screening
Q45407345	Design and characterization of an engineered gp41 protein from human immunodeficiency virus-1 as a tool for drug discovery
Q30873834	Design and characterization of chemical space networks for different compound data sets
Q54039496	Design and synthesis of type-III mimetics of ShK toxin.
Q74568399	Design and synthesis of type-III mimetics of omega-conotoxin GVIA
Q98652809	Design and tests of prospective property predictions for novel antimalarial 2-aminopropylaminoquinolones
Q78249929	Design criteria for molecular mimics of fragments of the beta-turn. 1. C alpha atom analysis
Q78249934	Design criteria for molecular mimics of fragments of the beta-turn. 2. C alpha-C beta bond vector analysis
Q33922101	Design of a colicin E7 based chimeric zinc-finger nuclease
Q33972623	Design of a fragment library that maximally represents available chemical space
Q33908733	Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics.
Q48230088	Design of a tripartite network for the prediction of drug targets
Q46939941	Design of an activity landscape view taking compound-based feature probabilities into account
Q35875854	Design of chemical space networks on the basis of Tversky similarity
Q86320243	Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures
Q33417723	Design of compound libraries for fragment screening
Q73558603	Design of dimerization inhibitors of HIV-1 aspartic proteinase: a computer-based combinatorial approach
Q33225368	Design of ligand binding to an engineered protein cavity using virtual screening and thermal up-shift evaluation.
Q115732709	Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing
Q43174214	Design of new secreted phospholipase A2 inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor
Q54334681	Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks.
Q57018486	Design of potential angiogenin inhibitors
Q40369005	Design of recombinant stem cell factor-macrophage colony stimulating factor fusion proteins and their biological activity in vitro
Q46614984	Design of stapled DNA-minor-groove-binding molecules with a mutable atom simulated annealing method
Q33543849	Design, structure-based focusing and in silico screening of combinatorial library of peptidomimetic inhibitors of Dengue virus NS2B-NS3 protease
Q35170923	Design, synthesis and experimental validation of novel potential chemopreventive agents using random forest and support vector machine binary classifiers
Q87139747	Design, synthesis and in vitro kinetic study of tranexamic acid prodrugs for the treatment of bleeding conditions
Q52587831	Designing novel nicotinic agonists by searching a database of molecular shapes.
Q77763158	Designing sedative/hypnotic compounds from a novel substructural graph-theoretical approach
Q39681302	Designing the molecular future
Q91134635	Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge
Q33466833	Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase
Q44291992	Detection of tautomer proportions of dimedone in solution: a new approach based on theoretical and FT-IR viewpoint
Q52531840	Determination of clefts in receptor structures.
Q71483788	Determination of receptor-bound drug conformations by QSAR using flexible fitting to derive a molecular similarity index
Q30664785	Developing 13C NMR quantitative spectrometric data-activity relationship (QSDAR) models of steroid binding to the corticosteroid binding globulin
Q35877995	Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions
Q52118228	Developing an in-house system to support combinatorial chemistry
Q33440704	Development and NMR validation of minimal pharmacophore hypotheses for the generation of fragment libraries enriched in heparanase inhibitors
Q33260986	Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors
Q33201132	Development and testing of a de novo drug-design algorithm
Q34588100	Development and validation of a modular, extensible docking program: DOCK 5.
Q42011227	Development and validation of an improved algorithm for overlaying flexible molecules
Q34647300	Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor
Q30915859	Development of QSAR models for microsomal stability: identification of good and bad structural features for rat, human and mouse microsomal stability
Q47393221	Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide.
Q44345689	Development of a common 3D pharmacophore for delta-opioid recognition from peptides and non-peptides using a novel computer program
Q44334810	Development of a conformational search strategy for flexible ligands: a study of the potent mu-selective opioid analgesic fentanyl
Q38967201	Development of a pharmacophore for cruzain using oxadiazoles as virtual molecular probes: quantitative structure-activity relationship studies
Q73331716	Development of a unique 3D interaction model of endogenous and synthetic peripheral benzodiazepine receptor ligands
Q52453050	Development of an automatic estimation system for both the partition coefficient and aqueous solubility.
Q44490741	Development of biologically active compounds by combining 3D QSAR and structure-based design methods
Q83178916	Development of energetic pharmacophore for the designing of 1,2,3,4-tetrahydropyrimidine derivatives as selective cyclooxygenase-2 inhibitors
Q80543755	Development of in silico models for human liver microsomal stability
Q30978307	Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors.
Q46344744	Development of purely structure-based pharmacophores for the topoisomerase I-DNA-ligand binding pocket
Q83172122	Development of small molecules designed to modulate protein-protein interactions
Q31106855	Development, interpretation and temporal evaluation of a global QSAR of hERG electrophysiology screening data
Q49177279	Different approaches toward an automatic structural alignment of drug molecules: applications to sterol mimics, thrombin and thermolysin inhibitors.
Q33323614	Differentiation of AmpC beta-lactamase binders vs. decoys using classification kNN QSAR modeling and application of the QSAR classifier to virtual screening
Q44335475	Differentiation of delta, mu, and kappa opioid receptor agonists based on pharmacophore development and computed physicochemical properties
Q47624951	Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania.
Q59576397	Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation
Q42274100	Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase.
Q58360607	Discovering New Classes of Brugia malayi Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change
Q57271321	Discovering high-affinity ligands from the computationally predicted structures and affinities of small molecules bound to a target: A virtual screening approach
Q48299334	Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening.
Q91150165	Discovery and evaluation of novel Mycobacterium tuberculosis ketol-acid reductoisomerase inhibitors as therapeutic drug leads
Q36100810	Discovery of DNA dyes Hoechst 34580 and 33342 as good candidates for inhibiting amyloid beta formation: in silico and in vitro study.
Q90824891	Discovery of a nanomolar inhibitor of the human glyoxalase-I enzyme using structure-based poly-pharmacophore modelling and molecular docking
Q43701180	Discovery of a novel serine protease inhibitor utilizing a structure-based and experimental selection of fragments technique
Q91406534	Discovery of a potential positive allosteric modulator of glucagon-like peptide 1 receptor through virtual screening and experimental study
Q52328849	Discovery of a small-molecule inhibitor of Dvl-CXXC5 interaction by computational approaches.
Q93119102	Discovery of new multifunctional selective acetylcholinesterase inhibitors: structure-based virtual screening and biological evaluation
Q47797733	Discovery of non-peptidic small molecule inhibitors of cyclophilin D as neuroprotective agents in Aβ-induced mitochondrial dysfunction
Q85066830	Discovery of novel human acrosin inhibitors by virtual screening
Q50200993	Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization.
Q91927626	Discovery of novel inhibitors of human galactokinase by virtual screening
Q40785976	Discovery of novel polyamine analogs with anti-protozoal activity by computer guided drug repositioning
Q91291275	Discovery of novel wee1 inhibitors via structure-based virtual screening and biological evaluation
Q33303858	Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches
Q47380200	Discovery of small molecules binding to the normal conformation of prion by combining virtual screening and multiple biological activity evaluation methods.
Q78743159	Discriminant and quantitative PLS analysis of competitive CYP2C9 inhibitors versus non-inhibitors using alignment independent GRIND descriptors
Q48238825	Disruptor of telomeric silencing 1-like (DOT1L): disclosing a new class of non-nucleoside inhibitors by means of ligand-based and structure-based approaches
Q91903974	Dissecting the molecular recognition of dual lapatinib derivatives for EGFR/HER2
Q41311286	Distance geometry analysis of ligand binding to drug receptor sites
Q47805558	Distant collaboration in drug discovery: the LINK3D project
Q30333075	Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening.
Q96642516	Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor H1
Q30406901	Distinct functional and conformational states of the human lymphoid tyrosine phosphatase catalytic domain can be targeted by choice of the inhibitor chemotype
Q57976081	Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
Q73913479	Diverse binding site structures revealed in homology models of polyreactive immunoglobulins
Q92584649	Diversifying chemical libraries with generative topographic mapping
Q77763153	Do active site conformations of small ligands correspond to low free-energy solution structures?
Q34566045	Do benzodiazepines mimic reverse-turn structures?
Q52453044	Do you believe in wavefunctions?
Q48280219	DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015.
Q80697148	Docking and multivariate methods to explore HIV-1 drug-resistance: a comparative analysis
Q83845170	Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2,3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine derivatives as c-Me
Q45162110	Docking and scoring of metallo-beta-lactamases inhibitors
Q36098710	Docking and scoring with ICM: the benchmarking results and strategies for improvement
Q33527932	Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function
Q38335016	Docking glycosaminoglycans to proteins: analysis of solvent inclusion
Q47797563	Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2.
Q28266363	Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide
Q39536628	Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015.
Q91561359	Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4
Q40525152	Docking simulations suggest that all-trans retinoic acid could bind to retinoid X receptors.
Q34415230	Docking studies on NSAID/COX-2 isozyme complexes using contact statistics analysis
Q44304349	Docking study of the precursor peptide of mastoparan onto its putative processing enzyme, dipeptidyl peptidase IV: a revisit to molecular ticketing
Q45184584	Docking-based CoMFA and CoMSIA studies of non-nucleoside reverse transcriptase inhibitors of the pyridinone derivative type
Q39317819	Docking-undocking combination applied to the D3R Grand Challenge 2015.
Q36243611	DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina
Q43555843	Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations
Q40985359	Does your model weigh the same as a duck?
Q38965242	Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates
Q89522959	Drug Design Data Resource, Grand Challenge 4, second of two issues
Q28732341	Drug design for ever, from hype to hope
Q33888145	Drug discovery using very large numbers of patents: general strategy with extensive use of match and edit operations
Q36082949	Drug search for leishmaniasis: a virtual screening approach by grid computing.
Q46121038	Drug-resistant molecular mechanism of CRF01_AE HIV-1 protease due to V82F mutation
Q34093054	Druggability of methyl-lysine binding sites
Q92566519	Druggable exosites of the human kino-pocketome
Q91135896	Dual-targeted hit identification using pharmacophore screening
Q41856129	Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble
Q33825866	Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer.
Q68049863	Dynamic simulation as an essential tool in molecular modeling
Q46720950	Dynamical aspects of TEM-1 beta-lactamase probed by molecular dynamics
Q86706640	Dynamics and structural determinants of ligand recognition of the 5-HT6 receptor
Q45102501	E-state fields: applications to 3D QSAR.
Q46788954	ENPDA: an evolutionary structure-based de novo peptide design algorithm.
Q73194557	EVA: a new theoretically based molecular descriptor for use in QSAR/QSPR analysis
Q51891050	Editorial: special issue on "Evaluation of computational methods".
Q44187754	Effect of pH and ligand charge state on BACE-1 fragment docking performance
Q33894051	Effect of training data size and noise level on support vector machines virtual screening of genotoxic compounds from large compound libraries
Q45944000	Effective prediction of bacterial type IV secreted effectors by combined features of both C-termini and N-termini.
Q46932255	Effective virtual screening protocol for CYP2C9 ligands using a screening site constructed from flurbiprofen and S-warfarin pockets
Q52033846	Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases.
Q36803981	Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC.
Q47730473	Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery
Q50278953	Effects of point mutations on the thermostability of B. subtilis lipase: investigating nonadditivity.
Q43115469	Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation
Q58855853	Effects of variable selection on CoMFA coefficient contour maps in a set of triazines inhibiting DHFR
Q37730016	Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK.
Q30155477	Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model
Q34575180	Efficient overlay of small organic molecules using 3D pharmacophores
Q50744649	Elaborate ligand-based modeling coupled with QSAR analysis and in silico screening reveal new potent acetylcholinesterase inhibitors.
Q50985589	Elaborate ligand-based modeling reveal new submicromolar Rho kinase inhibitors.
Q57976070	ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics
Q73798619	Electron affinities of p-benzoquinone, p-benzoquinone imine and p-benzoquinone diimine, and spin densities of their p-benzosemiquinones computed by several quantum chemical models
Q44871243	Electron-density-dependent fused-sphere surfaces derived from pseudopotential calculations
Q77447721	Electrostatic and structural similarity of classical and non-classical lactam compounds
Q57137396	Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects
Q52370120	Electrostatic complementarity between proteins and ligands. 2. Ligand moieties.
Q52370117	Electrostatic complementarity between proteins and ligands. 3. Structural basis.
Q33250369	Electrostatic evaluation of isosteric analogues
Q90934690	Electrostatic-field and surface-shape similarity for virtual screening and pose prediction
Q70232995	Electrostatics and computational modelling. Editorial overview
Q92475363	Elucidating the druggability of the human proteome with eFindSite
Q77763145	Elucidation of a common structure of selective fibrinogen receptor antagonists
Q45991103	Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes.
Q52230454	Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model.
Q53678858	Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.
Q31141737	Empowering pharmacoinformatics by linked life science data
Q114955379	Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning
Q39233769	Enabling drug discovery project decisions with integrated computational chemistry and informatics.
Q48137563	Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control.
Q44554590	Enantioselectivity of epoxide hydrolase catalysed oxirane ring opening: a 3D QSAR study.
Q30834193	Encouraging data citation and discovery with the Data Citation Index.
Q33440708	Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
Q83476926	Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir
Q68844981	Energy minimization and molecular dynamics studies of Asn-102 elastase
Q44699698	Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing
Q53504228	Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity.
Q33277028	Enhancement of chemical rules for predicting compound reactivity towards protein thiol groups
Q67976692	Enhancement of the solubilities of polycyclic aromatic hydrocarbons by weak hydrogen bonds with water
Q89949705	Enhancing reaction-based de novo design using a multi-label reaction class recommender
Q80988436	Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields
Q36794962	Enhancing the diversity of a corporate database using chemical database clustering and analysis
Q99618258	Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo
Q51070891	Ensemble pharmacophore meets ensemble docking: a novel screening strategy for the identification of RIPK1 inhibitors.
Q81360455	Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules
Q48244185	Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge
Q85959848	Erratum to: A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands
Q45064339	Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
Q86650052	Erratum to: design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures
Q53863505	Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories.
Q62489974	Estimating the domain of applicability for machine learning QSAR models: a study on aqueous solubility of drug discovery molecules
Q45964937	Estimating the domain of applicability for machine learning QSAR models: a study on aqueous solubility of drug discovery molecules.
Q78249937	Estimation of active conformations of drugs by a new molecular superposing procedure
Q30680780	Estimation of influential points in any data set from coefficient of determination and its leave-one-out cross-validated counterpart
Q50919565	Estimation of relative binding free energy based on a free energy variational principle for the FKBP-ligand system.
Q30662631	Estimation of the size of drug-like chemical space based on GDB-17 data.
Q51281674	EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC.
Q86188015	Euclidean chemical spaces from molecular fingerprints: Hamming distance and Hempel's ravens
Q46148600	Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities.
Q30367162	Evaluating docking programs: keeping the playing field level.
Q51482704	Evaluating the applicability domain in the case of classification predictive models for carcinogenicity based on the counter propagation artificial neural network.
Q93119111	Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures
Q33209809	Evaluation and application of multiple scoring functions for a virtual screening experiment
Q37518530	Evaluation of DOCK 6 as a pose generation and database enrichment tool
Q38558776	Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design
Q73798633	Evaluation of a novel infrared range vibration-based descriptor (EVA) for QSAR studies. 1. General application
Q77365348	Evaluation of a novel molecular vibration-based descriptor (EVA) for QSAR studies: 2. Model validation using a benchmark steroid dataset
Q80543481	Evaluation of descriptors and classification schemes to predict cytochrome substrates in terms of chemical information
Q43786252	Evaluation of designed ligands by a multiple screening method: application to glycogen phosphorylase inhibitors constructed with a variety of approaches
Q92763898	Evaluation of different virtual screening strategies on the basis of compound sets with characteristic core distributions and dissimilarity relationships
Q34104969	Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors
Q52076496	Evaluation of docking/scoring approaches: a comparative study based on MMP3 inhibitors.
Q44667599	Evaluation of extended parameter sets for the 3D-QSAR technique MaP: implications for interpretability and model quality exemplified by antimalarially active naphthylisoquinoline alkaloids
Q36700190	Evaluation of machine-learning methods for ligand-based virtual screening
Q112614220	Evaluation of multi-target deep neural network models for compound potency prediction under increasingly challenging test conditions
Q36897804	Evaluation of proposed modes of binding of (2S)-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxy]phenyl]-3-(7-am idino- 2- naphthyl)propanoic acid hydrochloride and some analogs to factor Xa using a comparative molecular field analysis
Q56986653	Evaluation of reactant-based and product-based approaches to the design of combinatorial libraries
Q52081435	Evaluation of the EVA descriptor for QSAR studies: 3. The use of a genetic algorithm to search for models with enhanced predictive properties (EVA_GA).
Q37057393	Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes?
Q40931321	Evolutionary algorithms in computer-aided molecular design
Q38720771	ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations
Q30358437	Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge.
Q83133195	Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction
Q100512761	Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds
Q43687591	Experimental design based 3-D QSAR analysis of steroid-protein interactions: application to human CBG complexes
Q46568237	Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation
Q86018664	Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling
Q60238413	Exploring ensembles of bioactive or virtual analogs of X-ray ligands for shape similarity searching
Q51911690	Exploring fragment spaces under multiple physicochemical constraints.
Q91292738	Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S
Q30875882	Exploring privileged structures: the combinatorial synthesis of cyclic peptides
Q48035411	Exploring sets of molecules from patents and relationships to other active compounds in chemical space networks
Q52652923	Exploring the dynamics and interaction of a full ErbB2 receptor and Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained force field.
Q56989244	Exploring the free-energy landscape of carbohydrate–protein complexes: development and validation of scoring functions considering the binding-site topology
Q90374506	Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach
Q44554593	Exploring the molecular basis of selectivity in A1 adenosine receptors agonists: a case study
Q39027957	Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations
Q49177145	Extended electron distributions applied to the molecular mechanics of some intermolecular interactions.
Q71851456	Extended electron distributions applied to the molecular mechanics of some intermolecular interactions. II. Organic complexes
Q43524484	Extended solvent-contact model approach to SAMPL4 blind prediction challenge for hydration free energies
Q39569522	Extended solvent-contact model approach to blind SAMPL5 prediction challenge for the distribution coefficients of drug-like molecules
Q72816270	Extending the trend vector: the trend matrix and sample-based partial least squares
Q48891681	Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.
Q91596904	Extensive benchmark of rDock as a peptide-protein docking tool
Q30423742	Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses.
Q53395167	Extracting ligands from receptors by reversed targeted molecular dynamics.
Q34415675	Extraction and validation of substructure profiles for enriching compound libraries
Q39116173	Extrapolative prediction using physically-based QSAR.
Q51643618	FILO (field interaction ligand optimization): a simplex strategy for searching the optimal ligand interaction field in drug design.
Q43786250	FLASHFLOOD: a 3D field-based similarity search and alignment method for flexible molecules
Q30420637	FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure
Q38565532	FOUNDATION: a program to retrieve all possible structures containing a user-defined minimum number of matching query elements from three-dimensional databases
Q51358561	FRED and HYBRID docking performance on standardized datasets.
Q43451646	FTree query construction for virtual screening: a statistical analysis.
Q30585007	Facet diagrams for quantum similarity data
Q58616267	Factor Xa: simulation studies with an eye to inhibitor design
Q91907393	Families and clans of cysteine peptidases
Q43594676	Fast 3D molecular superposition and similarity search in databases of flexible molecules
Q47845562	Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers
Q44247409	Fast and accurate methods for predicting short-range constraints in protein models
Q44325905	Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study.
Q52078631	Fast prediction and visualization of protein binding pockets with PASS.
Q45906417	Fast prediction of hydration free energies for SAMPL4 blind test from a classical density functional theory.
Q51647018	Feature trees: a new molecular similarity measure based on tree matching.
Q45965607	Feature-map vectors: a new class of informative descriptors for computational drug discovery.
Q78683432	Filtering databases and chemical libraries
Q38302057	Finding potential DNA-binding compounds by using molecular shape
Q52528201	Fine specificity of antigen binding to two class I major histocompatibility proteins (B2705 and B2703) differing in a single amino acid residue.
Q90857873	First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase
Q30834186	Fitting and handling dose response data
Q97533134	Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles
Q34319987	Flexibases: a way to enhance the use of molecular docking methods
Q34054640	Flexibility of a biotinylated ligand in artificial metalloenzymes based on streptavidin--an insight from molecular dynamics simulations with classical and ab initio force fields
Q44109232	Flexible docking under pharmacophore type constraints
Q52346365	Flexible ligand docking using a genetic algorithm.
Q71749028	Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: comparison of predicted and experimental conformations of inhibitors of three enzymes
Q30952629	Flexsim-R: a virtual affinity fingerprint descriptor to calculate similarities of functional groups
Q91063627	Focused Library Generator: case of Mdmx inhibitors
Q90101463	Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics
Q57057117	Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale
Q46419532	Force-field and quantum-mechanical binding study of selected SAMPL3 host-guest complexes
Q44896308	Force-field parametrization and molecular dynamics simulations of Congo red.
Q58225273	Force-field parametrization and molecular dynamics simulations of p-menthan-3,9-diols: a family of amphiphilic compounds derived from terpenoids
Q58224827	Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters
Q38909972	ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs
Q36438659	Forces in molecular recognition: comparison of experimental data and molecular mechanics calculations
Q41282224	Forging the future
Q74633111	Fractional description of free energies of solvation
Q35074986	Fragment-based Shape Signatures: a new tool for virtual screening and drug discovery
Q33474361	Fragment-based drug discovery
Q48438267	Fragment-based drug discovery: what really works. An interview with Sandy Farmer of Boehringer Ingelheim.
Q39731911	Fragment-based lead discovery: challenges and opportunities
Q33469688	Fragment-based lead generation: identification of seed fragments by a highly efficient fragment screening technology
Q46844812	Fragment-based prediction of skin sensitization using recursive partitioning.
Q35030073	Fragment-based strategy for structural optimization in combination with 3D-QSAR.
Q42956918	Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example
Q51550370	Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities.
Q43844939	Free energy force field (FEFF) 3D-QSAR analysis of a set of Plasmodium falciparum dihydrofolate reductase inhibitors
Q46628590	Free energy perturbation approach to the critical assessment of selective cyclooxygenase-2 inhibitors
Q57235415	Free enthalpies of replacing water molecules in protein binding pockets
Q87611444	Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies
Q28655211	FreeSolv: a database of experimental and calculated hydration free energies, with input files
Q45945153	From bird's eye views to molecular communities: two-layered visualization of structure-activity relationships in large compound data sets.
Q30657218	From data point timelines to a well curated data set, data mining of experimental data and chemical structure data from scientific articles, problems and possible solutions
Q83133107	Frozen out: molecular modeling in the age of cryocrystallography
Q58859728	Functional concerted motions in the bovine serum retinol-binding protein
Q30165525	Functional group placement in protein binding sites: a comparison of GRID and MCSS.
Q71483760	Functionality map analysis of the active site cleft of human thrombin
Q41103702	Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF): experimental and computational characterization
Q34526566	Further development and validation of empirical scoring functions for structure-based binding affinity prediction
Q41295404	Future in biomolecular computation
Q44348873	Future structural genomics initiatives: an interview with Helen Berman, director of the Protein Data Bank. Interview by Wendy A Warr
Q51930711	GALAHAD: 1. pharmacophore identification by hypermolecular alignment of ligands in 3D.
Q30925927	GEOM: a new tool for molecular modelling based on distance geometry calculations with NMR data
Q52373585	GREEN: a program package for docking studies in rational drug design.
Q58137119	GRIND-derived pharmacophore model for a series of α-tropanyl derivative ligands of the sigma-2 receptor*
Q47565870	GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking
Q51992733	Gaussian mapping of chemical fragments in ligand binding sites.
Q34076146	Gazing into the crystal ball; the future of computer-aided drug design
Q52401172	GenStar: a method for de novo drug design.
Q90703523	Generating conformational transition paths with low potential-energy barriers for proteins
Q58860144	Generation of a homology model of the human histamine H3 receptor for ligand docking and pharmacophore-based screening
Q51899915	Generation of in-silico cytochrome P450 1A2, 2C9, 2C19, 2D6, and 3A4 inhibition QSAR models.
Q46467172	Generation of multiple pharmacophore hypotheses using multiobjective optimisation techniques
Q31132887	Genetic algorithm for the design of molecules with desired properties
Q51536807	Genetic algorithms and self-organizing maps: a powerful combination for modeling complex QSAR and QSPR problems.
Q51245948	Genetic algorithms as a tool for helix design--computational and experimental studies on prion protein helix 1.
Q46865680	Genetic neural network modeling of the selective inhibition of the intermediate-conductance Ca2+ -activated K+ channel by some triarylmethanes using topological charge indexes descriptors.
Q69601240	Geometries of functional group interactions in enzyme-ligand complexes: guides for receptor modelling
Q40036944	Geometry optimization method versus predictive ability in QSPR modeling for ionic liquids
Q73652694	Global 3D-QSAR methods: MS-WHIM and autocorrelation
Q46328629	Glycogen synthase kinase-3 inhibition by 3-anilino-4-phenylmaleimides: insights from 3D-QSAR and docking
Q33317309	GridMol: a grid application for molecular modeling and visualization
Q80164054	Guest editorial for special issue on "ADME and Physical Properties"
Q30359360	Guidelines for the analysis of free energy calculations
Q48449691	Guiding effective decisions: an interview with Matthew Segall, CEO of Optibrium. Interview by Wendy A. Warr.
Q51074171	H-DROP: an SVM based helical domain linker predictor trained with features optimized by combining random forest and stepwise selection.
Q44194556	HEPT derivatives as non-nucleoside inhibitors of HIV-1 reverse transcriptase: QSAR studies agree with the crystal structures
Q44935041	HINT: a new method of empirical hydrophobic field calculation for CoMFA.
Q56395272	HTMoL: full-stack solution for remote access, visualization, and analysis of molecular dynamics trajectory data
Q48311195	Herman Skolnik award symposium honoring Yvonne Martin.
Q41105119	Heterofullerenes: structure and property predictions, possible uses and synthesis proposals
Q73913499	Heuristic lipophilicity potential for computer-aided rational drug design
Q77622454	Heuristic lipophilicity potential for computer-aided rational drug design: optimizations of screening functions and parameters
Q80642889	Hierarchical QSAR technology based on the Simplex representation of molecular structure
Q51937056	Hierarchical clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs.
Q91120392	High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge
Q43936132	High-affinity interactions of ligands at recombinant guinea pig 5HT7 receptors
Q33258784	High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening
Q69724839	Highly conformationally constrained halogenated 6-spiroepoxypenicillins as probes for the bioactive side-chain conformation of benzylpenicillin
Q46382445	Homo-timeric structural model of human microsomal prostaglandin E synthase-1 and characterization of its substrate/inhibitor binding interactions
Q73558607	Homology model directed alignment selection for comparative molecular field analysis: application to photosystem II inhibitors
Q51680712	Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0.
Q45140752	Homology modeling and molecular dynamics simulation of N-myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design
Q46630846	Homology modeling and molecular interaction field studies of alpha-glucosidases as a guide to structure-based design of novel proposed anti-HIV inhibitors.
Q42643877	Homology modeling of 5-lipoxygenase and hints for better inhibitor design
Q77622447	Homology modeling of the receptor binding domain of human thrombopoietin
Q84325850	Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase
Q45232745	Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors
Q43276048	Homology modelling of the human adenosine A2B receptor based on X-ray structures of bovine rhodopsin, the beta2-adrenergic receptor and the human adenosine A2A receptor
Q72137028	HomologyPlot: searching for homology to a family of proteins using a database of unique conserved patterns
Q58023183	Host andPorphyromonas gingivalis proteinases in periodontitis: A biochemical model of infection and tissue destruction
Q89690119	How N-(pyridin-4-yl)pyridin-4-amine and its methyl and nitro derivatives are arranged in the interlayer space of zirconium sulfophenylphosphonate: a problem solved by experimental and calculation methods
Q47793987	How accurate are continuum solvation models for drug-like molecules?
Q92763888	How computational chemistry develops: a tribute to Peter Goodford
Q90303607	How medicinal chemists learned about log P
Q84958923	How the energy evaluation method used in the geometry optimization step affect the quality of the subsequent QSAR/QSPR models
Q30952705	How to acquire new biological activities in old compounds by computer prediction.
Q37064087	How to do an evaluation: pitfalls and traps
Q94083406	How to do an evaluation: pitfalls and traps
Q87313284	Human farnesyl pyrophosphate synthase inhibition by nitrogen bisphosphonates: a 3D-QSAR study
Q46630855	Human topoisomerase I poisoning: docking protoberberines into a structure-based binding site model
Q90863654	Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3
Q71491557	Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions
Q71491560	Hydration in drug design. 2. Influence of local site surface shape on water binding
Q53903013	Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins.
Q57752850	Hydration of beta-cyclodextrin: a molecular dynamics simulation study
Q73233704	Hydrogen bonding and dimeric self-association of 2-pyrrolidinone: an ab initio study
Q52376641	Hydrophile-lipophile balance of alkyl ethoxylated surfactants as a function of intermolecular energies.
Q46758100	Hydrophobic molecular similarity from MST fractional contributions to the octanol/water partition coefficient.
Q48593386	IA, database of known ligands of aminoacyl-tRNA synthetases.
Q56918926	IADE: a system for intelligent automatic design of bioisosteric analogs
Q44779922	IS-Dom: a dataset of independent structural domains automatically delineated from protein structures
Q52234494	Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase.
Q89630929	Identification and neuroprotective evaluation of a potential c-Jun N-terminal kinase 3 inhibitor through structure-based virtual screening and in-vitro assay
Q38942084	Identification of antipsychotic drug fluspirilene as a potential p53-MDM2 inhibitor: a combined computational and experimental study
Q53365053	Identification of common inhibitors of wild-type and T315I mutant of BCR-ABL through the parallel structure-based virtual screening.
Q43631523	Identification of cylin-dependent kinase 1 inhibitors of a new chemical type by structure-based design and database searching
Q30378289	Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development.
Q33472769	Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications
Q54313399	Identification of ligand efficient, fragment-like hits from an HTS library: structure-based virtual screening and docking investigations of 2H- and 3H-pyrazolo tautomers for Aurora kinase A selectivity.
Q41751942	Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR.
Q42991468	Identification of ligands that target the HCV-E2 binding site on CD81.
Q36171916	Identification of novel Trypanosoma cruzi prolyl oligopeptidase inhibitors by structure-based virtual screening.
Q92533317	Identification of novel and potent small-molecule inhibitors of tubulin with antitumor activities by virtual screening and biological evaluations
Q41035643	Identification of novel inhibitors for Pim-1 kinase using pharmacophore modeling based on a novel method for selecting pharmacophore generation subsets.
Q35329233	Identification of novel inhibitors of human Chk1 using pharmacophore-based virtual screening and their evaluation as potential anti-cancer agents.
Q53425325	Identification of novel inhibitors of mitogen-activated protein kinase phosphatase-1 with structure-based virtual screening.
Q35234394	Identification of novel peroxisome proliferator-activated receptor-gamma (PPARγ) agonists using molecular modeling method.
Q34691787	Identification of novel small molecule TGF-β antagonists using structure-based drug design
Q40396412	Identification of novel target sites and an inhibitor of the dengue virus E protein
Q91255146	Identification of protoberberine alkaloids as novel histone methyltransferase G9a inhibitors by structure-based virtual screening
Q31068979	Identification of target-specific bioisosteric fragments from ligand-protein crystallographic data
Q41921115	Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations
Q34458951	Identification of tissue-specific targeting peptide
Q33400428	Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators
Q30409188	Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics
Q44087623	Identifying potential binding modes and explaining partitioning behavior using flexible alignments and multidimensional scaling
Q47604123	Identifying the binding mode of a molecular scaffold.
Q35714235	If we designed airplanes like we design drugs....
Q45991101	Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure-activity relationships and molecular docking.
Q45747848	Impact of distance-based metric learning on classification and visualization model performance and structure-activity landscapes.
Q47406205	Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations
Q49349893	Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide.
Q51963745	Implementation of smooth continuous camera trajectories for viewing PDB and VRML objects.
Q40675058	Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants.
Q43805829	Improved convergence of binding affinities with free energy perturbation: application to nonpeptide ligands with pp60src SH2 domain
Q33573726	Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles
Q42739070	Improved estimation of ligand-macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods
Q30844880	Improved mapping of protein binding sites
Q31135416	Improved pose and affinity predictions using different protocols tailored on the basis of data availability
Q38698230	Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015.
Q80642884	Improving database enrichment through ensemble docking
Q30369696	Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions.
Q92971717	Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model
Q51500330	Improving molecular docking through eHiTS' tunable scoring function.
Q39187331	Improving quantitative structure-activity relationship models using Artificial Neural Networks trained with dropout
Q57976069	Improving the accuracy of ultrafast ligand-based screening: incorporating lipophilicity into ElectroShape as an extra dimension
Q90416653	Improving the binding affinity estimations of protein-ligand complexes using machine-learning facilitated force field method
Q115732708	Imputation of sensory properties using deep learning
Q34194604	In memoriam professor Corwin Hansch: birth pangs of QSAR before 1961.
Q30351707	In search of new lead compounds for trypanosomiasis drug design: a protein structure-based linked-fragment approach.
Q28820807	In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor
Q35292182	In silico ADME/Tox: why models fail
Q42979856	In silico analysis of the histaprodifen induced activation pathway of the guinea-pig histamine H(1)-receptor
Q91343393	In silico fragment-mapping method: a new tool for fragment-based/structure-based drug discovery
Q42730804	In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases
Q38302099	In silico identification of novel ligands for G-quadruplex in the c-MYC promoter
Q39428478	In silico inspired design and synthesis of a novel tubulin-binding anti-cancer drug: folate conjugated noscapine (Targetin).
Q46111336	In silico model for P-glycoprotein substrate prediction: insights from molecular dynamics and in vitro studies
Q33202593	In silico models for the prediction of dose-dependent human hepatotoxicity
Q43658463	In silico molecular docking analysis of the human Argonaute 2 PAZ domain reveals insights into RNA interference.
Q82283376	In silico prediction of acyl glucuronide reactivity
Q31165898	In silico prediction of drug toxicity
Q47844404	In silico probing and biological evaluation of SETDB1/ESET-targeted novel compounds that reduce tri-methylated histone H3K9 (H3K9me3) level
Q44554597	In silico rationalization of the structural and physicochemical requirements for photobiological activity in angelicine derivatives and their heteroanalogues
Q34785012	In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors
Q61445645	In silico strategies for the selection of chelating compounds with potential application in metal-promoted neurodegenerative diseases
Q48439351	In tribute to Corwin Hansch, father of QSAR.
Q53076975	In-silico guided discovery of novel CCR9 antagonists.
Q52566240	In-silico screening using flexible ligand binding pockets: a molecular dynamics-based approach.
Q36606981	Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling
Q42673544	Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein.
Q51925745	Incorporating partial matches within multi-objective pharmacophore identification.
Q47808756	Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles
Q48044225	Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks
Q73013897	Indices of differences of path lengths: novel topological descriptors derived from electronic interferences in graphs
Q93383642	Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction
Q85888112	Inflation of correlation in the pursuit of drug-likeness
Q46808355	Influence of conformation on the representation of small flexible molecules at low resolution: alignment of endothiapepsin ligands.
Q92360805	Influence of feature rankers in the construction of molecular activity prediction models
Q89450851	Influence of gauche effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies
Q42922783	Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum study
Q47276113	Inhibition and substrate recognition--a computational approach applied to HIV protease
Q90020262	Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking
Q91624899	Inhibitor discovery for the E. coli meningitis virulence factor IbeA from homology modeling and virtual screening
Q72933425	Inhibitors of prolyl endopeptidase: characterization of the pharmacophoric pattern using conformational analysis and 3D-QSAR
Q57781255	Insight into microtubule destabilization mechanism of 3,4,5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis
Q42182937	Insight into the modified Ibalizumab-human CD4 receptor interactions: using a computational binding free energy approach
Q49722085	Insight into the molecular mechanism of yeast acetyl-coenzyme A carboxylase mutants F510I, N485G, I69E, E477R, and K73R resistant to soraphen A.
Q40911493	Insights into resistance mechanism of the macrolide biosensor protein MphR(A) binding to macrolide antibiotic erythromycin by molecular dynamics simulation
Q93173606	Insights into the EGFR SAR of N-phenylquinazolin-4-amine-derivatives using quantum mechanical pairwise-interaction energies
Q42906910	Insights into the binding mode and mechanism of action of some atypical retinoids as ligands of the small heterodimer partner (SHP).
Q37589537	Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models
Q41629853	Insights into the preferential order of strand exchange in the Cre/loxP recombinase system: impact of the DNA spacer flanking sequence and flexibility
Q51330280	Integrated in silico approaches for the prediction of Ames test mutagenicity.
Q79804490	Interaction force diagrams: new insight into ligand-receptor binding
Q83025440	Interaction of clozapine and its nitrenium ion with rat D2 dopamine receptors: in vitro binding and computational study
Q39465346	Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015.
Q43975038	Interactions between anti-ErbB2 antibody A21 and the ErbB2 extracellular domain provide a basis for improving A21 affinity
Q46155298	Interactions between cycloguanil derivatives and wild type and resistance-associated mutant Plasmodium falciparum dihydrofolate reductases
Q100428437	Interactions of GF-17 derived from LL-37 antimicrobial peptide with bacterial membranes: a molecular dynamics simulation study
Q46454089	Interactions of peptide mimics of hyaluronic acid with the receptor for hyaluronan mediated motility (RHAMM).
Q46159218	Interactive essential dynamics
Q85815370	Intermediate states in the binding process of folic acid to folate receptor α: insights by molecular dynamics and metadynamics
Q44109235	Internally defined distances in 3D-quantitative structure-activity relationships
Q94497353	Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions
Q30967921	Interpreting physicochemical experimental data sets
Q27681778	Interrogating HIV integrase for compounds that bind- a SAMPL challenge
Q41504204	Introducing the 'active search' method for iterative virtual screening
Q46157145	Introduction to the special issue: Data Part 2: Experimental Data
Q58108982	Investigating cyclic peptides inhibiting CD2-CD58 interactions through molecular dynamics and molecular docking methods
Q45994451	Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors.
Q44895743	Investigating the hydrogen-bond acceptor site of the nicotinic pharmacophore model: a computational and experimental study using epibatidine-related molecular probes
Q30648918	Investigation of classification methods for the prediction of activity in diverse chemical libraries
Q47797187	Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics.
Q28246874	Investigation of substituent effect of 1-(3,3-diphenylpropyl)-piperidinyl phenylacetamides on CCR5 binding affinity using QSAR and virtual screening techniques
Q52643202	Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations.
Q47581478	Investigation of the intermolecular recognition mechanism between the E3 ubiquitin ligase Keap1 and substrate based on multiple substrates analysis.
Q44167538	Investigation of the metal binding site in methionine aminopeptidase by density functional theory.
Q96957947	Investigations on the E/Z-isomerism of neonicotinoids
Q48263627	Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds?
Q73604198	Is the parallel or antiparallel beta-sheet more stable? A semiempirical study
Q39684964	Is there a future for computational chemistry in drug research?
Q32103649	IsoStar: a library of information about nonbonded interactions
Q51062863	JCAMD special series: statistics and molecular modeling.
Q52013586	Key issues in the computational simulation of GPCR function: representation of loop domains.
Q28829862	Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design
Q37544381	Knowing when to give up: early-rejection stratagems in ligand docking
Q35621988	Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock
Q45964832	LASSO-ligand activity by surface similarity order: a new tool for ligand based virtual screening.
Q52346358	LFER and CoMFA studies on optical resolution of alpha-alkyl alpha-aryloxy acetic acid methyl esters on DACH-DNB chiral stationary phase.
Q44114180	LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
Q39453218	Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
Q90716418	Large-scale evaluation of cytochrome P450 2C9 mediated drug interaction potential with machine learning-based consensus modeling
Q28266243	Lead Finder docking and virtual screening evaluation with Astex and DUD test sets
Q30410587	Lead optimization mapper: automating free energy calculations for lead optimization
Q33276455	Lead-like, drug-like or "Pub-like": how different are they?
Q45942993	Learning epistatic interactions from sequence-activity data to predict enantioselectivity.
Q49349899	Leaving us with fond memories, smiles, SMILES and, alas, tears: a tribute to David Weininger, 1952-2016.
Q30864260	Lessons for fragment library design: analysis of output from multiple screening campaigns
Q30275590	Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
Q47359129	Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor.
Q38899445	Lessons learned from the design of chemical space networks and opportunities for new applications
Q47414331	Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2.
Q51604998	Let's get honest about sampling.
Q33511462	Let's not forget tautomers
Q37464148	Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands
Q67508426	Ligand atom partial charges assignment for complementary electrostatic potentials
Q74505232	Ligand binding affinity prediction by linear interaction energy methods
Q47622535	Ligand binding to domain-3 of human serum albumin: a chemometric analysis
Q33291961	Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4.
Q40898209	Ligand docking and binding site analysis with PyMOL and Autodock/Vina
Q88019760	Ligand efficiency metrics considered harmful
Q44720168	Ligand expansion in ligand-based virtual screening using relevance feedback
Q80566722	Ligand intramolecular motions in ligand-protein interaction: ALPHA, a novel dynamic descriptor and a QSAR study with extended steroid benchmark dataset
Q50888328	Ligand- and receptor-based docking with LiBELa.
Q59489014	Ligand-, structure- and pharmacophore-based molecular fingerprints: a case study on adenosine A1, A2A, A2B, and A3 receptor antagonists
Q112693388	Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal
Q38896131	Ligand-based virtual screening under partial shape constraints
Q45942240	Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.
Q44789723	Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach.
Q52066525	Ligand-receptor docking with the Mining Minima optimizer.
Q41283780	Limiting assumptions in molecular modeling: electrostatics
Q37972732	Limiting assumptions in structure-based design: binding entropy
Q80405218	Linear and nonlinear functions on modeling of aqueous solubility of organic compounds by two structure representation methods
Q28732338	Lions and tigers and bears, oh my! Three barriers to progress in computer-aided molecular design
Q34209458	Lipophilicity in PK design: methyl, ethyl, futile
Q34309917	Local elevation: a method for improving the searching properties of molecular dynamics simulation.
Q33819815	Local neighborhood behavior in a combinatorial library context
Q73013881	Localization and quantification of hydrophobicity: the molecular free energy density (MolFESD) concept and its application to sweetness recognition
Q52056851	Locally linear embedding for dimensionality reduction in QSAR.
Q92650826	LogP prediction performance with the SMD solvation model and the M06 density functional family for SAMPL6 blind prediction challenge molecules
Q48496292	Looking forward into the next 25 years: the 25th anniversary issue of the Journal of Computer-Aided Molecular Design.
Q52340891	MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry.
Q44667593	MCASE study of the multidrug resistance reversal activity of propafenone analogs
Q78249919	MCDOCK: a Monte Carlo simulation approach to the molecular docking problem
Q36438656	MENTHOR, a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural, biologic, physical, or geometric properties
Q51652885	MEPSIM: a computational package for analysis and comparison of molecular electrostatic potentials.
Q35159035	MLP Tools: a PyMOL plugin for using the molecular lipophilicity potential in computer-aided drug design
Q82599858	MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model
Q73315110	MM3(96) parameterization for camptothecin analogs: an ab initio and molecular mechanics study
Q87428553	MOOCers and shakers and chemistry course takers
Q37328051	MOPAC: a semiempirical molecular orbital program
Q73315115	MS-WHIM, new 3D theoretical descriptors derived from molecular surface properties: a comparative 3D QSAR study in a series of steroids
Q47742327	MTD-ADJ: a multiconformational minimal topologic difference for determining bioactive conformers using adjusted biological activities
Q45963769	Machine learning of chemical reactivity from databases of organic reactions.
Q45962041	Machine learning study for the prediction of transdermal peptide.
Q100505468	Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications
Q90623080	Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4
Q38326787	Major versus minor groove DNA binding of a bisarginylporphyrin hybrid molecule: a molecular mechanics investigation
Q39826842	Making priors a priority
Q53033714	Managing bias in ROC curves.
Q34667555	Managing missing measurements in small-molecule screens.
Q27943500	Many InChIs and quite some feat
Q40325980	Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds
Q53332785	Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry.
Q47604098	Mapping protein pockets through their potential small-molecule binding volumes: QSCD applied to biological protein structures
Q51007235	Markov model-based polymer assembly from force field-parameterized building blocks.
Q30791792	Matching organic libraries with protein-substructures.
Q91309178	MathDL: mathematical deep learning for D3R Grand Challenge 4
Q63244985	Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges
Q35037939	Maximum common subgraph isomorphism algorithms for the matching of chemical structures
Q50596276	Maximum common substructure-based Tversky index: an asymmetric hybrid similarity measure.
Q81437644	Measuring CAMD technique performance: a virtual screening case study in the design of validation experiments
Q38813544	Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge
Q73010973	Mechanism of action of aspartic proteinases: application of transition-state analogue theory
Q54578344	Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling.
Q50503846	Mechanism of falcipain-2 inhibition by α,β-unsaturated benzo[1,4]diazepin-2-one methyl ester.
Q80800641	Mechanism of inhibition of human secretory phospholipase A2 by flavonoids: rationale for lead design
Q42941894	Mechanisms of amphipathic helical peptide denaturation by guanidinium chloride and urea: a molecular dynamics simulation study.
Q85390872	Mechanistic insights into protonation state as a critical factor in hFPPS enzyme inhibition
Q30778898	Megavariate analysis of hierarchical QSAR data
Q96582928	Meta-iPVP: a sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation
Q44325908	Metal complexes of chiral pentaazacrowns as conformational templates for beta-turn recognition
Q30656461	Methodological developments and strategies for a fast flexible superposition of drug-size molecules
Q36373060	Milestones in electron crystallography
Q52078633	Mixed QM/MM molecular electrostatic potentials.
Q45372748	Mixed learning algorithms and features ensemble in hepatotoxicity prediction.
Q31112333	Model based on GRID-derived descriptors for estimating CYP3A4 enzyme stability of potential drug candidates
Q64910935	Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design.
Q30395805	Modeling & Informatics at Vertex Pharmaceuticals Incorporated: our philosophy for sustained impact.
Q97675058	Modeling Epac1 interactions with the allosteric inhibitor AM-001 by co-solvent molecular dynamics
Q33647180	Modeling activated states of GPCRs: the rhodopsin template
Q60429767	Modeling activated states of GPCRs: the rhodopsin template
Q79280850	Modeling and active site refinement for G protein-coupled receptors: application to the beta-2 adrenergic receptor
Q52435960	Modeling and conformation analysis of beta-cyclodextrin complexes.
Q33270297	Modeling chemical reactions for drug design
Q51891051	Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations.
Q30367791	Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies.
Q27316009	Modeling ligand recognition at the P2Y12 receptor in light of X-ray structural information
Q44866867	Modeling lipophilicity from the distribution of electrostatic potential on a molecular surface
Q34288765	Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10.
Q51812818	Modeling of peptides containing D-amino acids: implications on cyclization.
Q68559274	Modeling of protease I collagenolytic enzyme from the fiddler crab Uca pugilator
Q83450537	Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function
Q36503781	Modeling the evolution of drug resistance in malaria
Q33309679	Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives
Q40775373	Modeling the interactions of a peptide-major histocompatibility class I ligand with its receptors. I. Recognition by two alpha beta T cell receptors
Q42620546	Modeling the interactions of a peptide-major histocompatibility class I ligand with its receptors. II. Cross-reaction between a monoclonal antibody and two alpha beta T cell receptors.
Q34063351	Modeling the pharmacodynamics of passive membrane permeability
Q77428754	Modelling a 3D structure for EgDf1 from Echinococcus granulosus: putative epitopes, phosphorylation motifs and ligand
Q70790871	Modelling and mutation studies on the histamine H1-receptor agonist binding site reveal different binding modes for H1-agonists: Asp116 (TM3) has a constitutive role in receptor stimulation
Q74625546	Modelling of adrenoceptor ligand targets based on novel medium- or macro-sized fused nitrogen heterocyclic systems
Q68846654	Modelling of alpha-lactalbumin from the known structure of hen egg white lysozyme using molecular dynamics
Q58491302	Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance
Q73798615	Modelling of the binding site of the human m1 muscarinic receptor: experimental validation and refinement
Q52289432	Modelling steric effects in DNA-binding platinum(II)-am(m)ine complexes.
Q71491544	Modelling study of protein kinase inhibitors: binding mode of staurosporine and origin of the selectivity of CGP 52411
Q46758094	Modelling the interaction of catecholamines with the alpha 1A adrenoceptor towards a ligand-induced receptor structure.
Q68121890	Models for the binding of amiodarone to the thyroid hormone receptor
Q30371590	Models of protein-ligand crystal structures: trust, but verify
Q45943917	Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations.
Q44109231	Modified AutoDock for accurate docking of protein kinase inhibitors
Q47820341	MolAlign: an algorithm for aligning multiple small molecules.
Q42373393	Molden 2.0: quantum chemistry meets proteins
Q50694018	Molden: a pre- and post-processing program for molecular and electronic structures.
Q82663150	Molecular and structural determinants of adamantyl susceptibility to HLA-DRs allelic variants: an in silico approach to understand the mechanism of MLEs
Q48043854	Molecular basis of P450 OleTJE: an investigation of substrate binding mechanism and major pathways.
Q52217017	Molecular basis of quantitative structure-properties relationships (QSPR): a quantum similarity approach.
Q46628594	Molecular design of two sterol 14alpha-demethylase homology models and their interactions with the azole antifungals ketoconazole and bifonazole
Q68329869	Molecular determinants in the bioactivation of the dopaminergic neurotoxin N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)
Q39725235	Molecular docking and 3D-quantitative structure activity relationship analyses of peptidyl vinyl sulfones: Plasmodium Falciparum cysteine proteases inhibitors.
Q43248352	Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin
Q39325646	Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets
Q44115744	Molecular docking studies of a group of hydroxamate inhibitors with gelatinase-A by molecular dynamics
Q45247134	Molecular docking studies on tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepinone (TIBO) derivatives as HIV-1 NNRT inhibitors
Q83943548	Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling
Q59576097	Molecular dynamics characterization of the SAMHD1 Aicardi–Goutières Arg145Gln mutant: structural determinants for the impaired tetramerization
Q38417439	Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking: anchors modified polyanions interference with the HIV-1 fusion mediator
Q43979135	Molecular dynamics of 5-HT1A and 5-HT2A serotonin receptors with methylated buspirone analogues.
Q60998748	Molecular dynamics of Mycobacterium tuberculosis KasA: implications for inhibitor and substrate binding and consequences for drug design
Q43703243	Molecular dynamics simulation and linear interaction energy study of D-Glu-based inhibitors of the MurD ligase
Q69464713	Molecular dynamics simulation as a complement to diffraction in the study of disorder in crystals
Q33481737	Molecular dynamics simulation of S100B protein to explore ligand blockage of the interaction with p53 protein
Q73041072	Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A)
Q30863658	Molecular dynamics simulation of halogen bonding mimics experimental data for cathepsin L inhibition
Q47655089	Molecular dynamics simulation of matrix metalloproteinase 2: fluctuations and time evolution of recognition pockets
Q55042750	Molecular dynamics simulation of the human adenosine A3 receptor: agonist induced conformational changes of Trp243.
Q53859885	Molecular dynamics simulation of the ligand binding domain of mGluR1 in response to agonist and antagonist binding.
Q57138268	Molecular dynamics simulation of the renin inhibitor H142 in water
Q46441558	Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling
Q51678306	Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions.
Q36852484	Molecular dynamics simulations give insight into D-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase
Q36461086	Molecular dynamics simulations of cyclosporin A: the crystal structure and dynamic modelling of a structure in apolar solution based on NMR data
Q38782160	Molecular dynamics simulations of halide glasses
Q46642485	Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein.
Q72816267	Molecular dynamics simulations of oligonucleotides in solution: visualization of intrinsic curvature
Q83978827	Molecular dynamics simulations of pro-apoptotic BH3 peptide helices in aqueous medium: relationship between helix stability and their binding affinities to the anti-apoptotic protein Bcl-X(L)
Q79280859	Molecular dynamics simulations on the inhibition of cyclin-dependent kinases 2 and 5 in the presence of activators
Q58327982	Molecular dynamics studies of α-helix stability in fibril-forming peptides
Q47604133	Molecular dynamics study of peptide segments of the BH3 domain of the proapoptotic proteins Bak, Bax, Bid and Hrk bound to the Bcl-xL and Bcl-2 proteins.
Q35623525	Molecular dynamics to enhance structure-based virtual screening on cathepsin B.
Q36819901	Molecular dynamics: deciphering the data
Q78043568	Molecular electrostatic potentials as input for the alignment of HIV-1 integrase inhibitors in 3D QSAR
Q38828100	Molecular graph convolutions: moving beyond fingerprints.
Q46698360	Molecular insight into γ-γ tubulin lateral interactions within the γ-tubulin ring complex (γ-TuRC).
Q88052698	Molecular insight of isotypes specific β-tubulin interaction of tubulin heterodimer with noscapinoids
Q62631468	Molecular insight on the non-covalent interactions between carbapenems and l,d-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study
Q68248935	Molecular level model for the agonist/antagonist selectivity of the 1,4-dihydropyridine calcium channel receptor
Q52379524	Molecular lipophilicity potential, a tool in 3D QSAR: method and applications.
Q52544096	Molecular mechanics calculations on deaminooxytocin and on deamino-arginine-vasopressin and its analogues.
Q51325445	Molecular mechanism of R-bicalutamide switching from androgen receptor antagonist to agonist induced by amino acid mutations using molecular dynamics simulations and free energy calculation.
Q44667602	Molecular model of the neural dopamine transporter
Q56784778	Molecular modeling and bioinformatical analysis of the antibacterial target enzyme MurA from a drug design perspective
Q58846797	Molecular modeling and dynamics of neuropeptide Y
Q63916872	Molecular modeling of a putative antagonist binding site on helix III of the β-adrenoceptor
Q43909373	Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar
Q73604191	Molecular modeling of cytochrome P450 3A4
Q44087626	Molecular modeling of interactions of the non-peptide antagonist YM087 with the human vasopressin V1a, V2 receptors and with oxytocin receptors.
Q30403920	Molecular modeling of protein structure and function: a bioinformatic approach
Q77336349	Molecular modeling of the human vasopressin V2 receptor/agonist complex
Q41061215	Molecular modeling of the intestinal bile acid carrier: a comparative molecular field analysis study
Q48633791	Molecular modeling of the neurophysin I/oxytocin complex.
Q30363533	Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors.
Q45150390	Molecular modeling studies on the urease active site and the enzyme-catalyzed urea hydrolysis
Q44352483	Molecular modeling study of the differential ligand-receptor interaction at the mu, delta and kappa opioid receptors
Q39025426	Molecular modeling study of the induced-fit effect on kinase inhibition: the case of fibroblast growth factor receptor 3 (FGFR3).
Q77622443	Molecular modeling study of tubulosine and other related ipecac alkaloids
Q71483776	Molecular modelling and conformational analysis of a GABAB antagonist
Q33389197	Molecular modelling evaluation of the cytotoxic activity of podophyllotoxin analogues
Q39568002	Molecular modelling in design of crop protection chemicals
Q68665073	Molecular modelling of poly(aryl ether ketones). I. Aryl..aryl interactions in crystal structures
Q31131948	Molecular modelling prediction of ligand binding site flexibility
Q67865138	Molecular modelling studies and the chromatographic behaviour of oxiracetam and some closely related molecules
Q57948799	Molecular modelling studies of substrate binding to the lipase from Rhizomucor miehei
Q47796479	Molecular modelling studies on the ORL1-receptor and ORL1-agonists
Q77763142	Molecular moment similarity between clozapine and substituted [(4-phenylpiperazinyl)-methyl] benzamides: selective dopamine D4 agonists
Q37843834	Molecular motions in drug design: the coming age of the metadynamics method
Q52838984	Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation.
Q81575893	Molecular shape and electrostatics in the encoding of relevant chemical information
Q68665067	Molecular similarity: the introduction of flexible fitting
Q54508458	Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes.
Q40415323	Molecular simulation assisted identification of Ca(2+) binding residues in TMEM16A.
Q39676629	Molecular simulation methods in drug discovery: a prospective outlook
Q43480285	Molecular structure matching by simulated annealing. I. A comparison between different cooling schedules
Q68665077	Molecular structure matching by simulated annealing. II. An exploration of the evolution of configuration landscape problems
Q52453058	Molecular structure matching by simulated annealing. III. The incorporation of null correspondences into the matching problem.
Q44087939	Molecular structure matching by simulated annealing. IV. Classification of atom correspondences in sets of dissimilar molecules
Q52321861	Molecular surface-volume and property matching to superpose flexible dissimilar molecules.
Q98565059	Monomer structure fingerprints: an extension of the monomer composition version for peptide databases
Q93023479	Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge
Q30847414	Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition
Q89724286	Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge
Q115732710	Multi-task convolutional neural networks for predicting in vitro clearance endpoints from molecular images
Q91438187	Multi-task generative topographic mapping in virtual screening
Q44361690	Multi-task learning for pKa prediction
Q70790863	Multiconformational composite molecular potential fields in the analysis of drug action. I. Methodology and first evaluation using 5-HT and histamine action as examples
Q30875856	Multiobjective optimization of combinatorial libraries
Q52260133	Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention.
Q84230608	Multiple ligand docking by Glide: implications for virtual second-site screening
Q46628596	Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase
Q80697151	Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results
Q38670015	Multiple receptor-ligand based pharmacophore modeling and molecular docking to screen the selective inhibitors of matrix metalloproteinase-9 from natural products
Q58137155	Multivariate analysis of experimental and computational descriptors of molecular lipophilicity
Q42256315	Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study
Q100729202	Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics
Q58114859	Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors
Q34871486	NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41.
Q38302873	NMR-restrained docking of a peptidic inhibitor to the N-terminal domain of the phosphoenolpyruvate:sugar phosphotransferase enzyme I.
Q90814699	Network-based piecewise linear regression for QSAR modelling
Q67891436	Networks
Q51890925	Neural network-based QSAR and insecticide discovery: spinetoram.
Q43844943	Neuronal nicotinic receptor agonists: a multi-approach development of the pharmacophore
Q56978998	New 3D molecular descriptors: the WHIM theory and QSAR applications
Q57460266	New approaches to QSAR: Neural networks and machine learning
Q47276095	New atom-type-based AI topological indices: application to QSPR studies of aldehydes and ketones
Q53851119	New designs for MRI contrast agents.
Q51638309	New developments in PEST shape/property hybrid descriptors.
Q43021736	New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface
Q85651588	New insights from molecular dynamic simulation studies of the multiple binding modes of a ligand with G-quadruplex DNA
Q43047168	New insights into flavivirus biology: the influence of pH over interactions between prM and E proteins.
Q50576810	New insights into human farnesyl pyrophosphate synthase inhibition by second-generation bisphosphonate drugs.
Q40177843	New insights into the stereochemical requirements of the bradykinin B2 receptor antagonists binding
Q45261846	New leads for selective GSK-3 inhibition: pharmacophore mapping and virtual screening studies
Q78683448	New methods in predictive metabolism
Q46652883	New molecular shape descriptors: application in database screening
Q69475767	New products and rumors of new products
Q102370437	Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software
Q91455965	Non-zero Lennard-Jones parameters for the Toukan-Rahman water model: more accurate calculations of the solvation free energy of organic substances
Q70661459	Nonlinear dependence in comparative molecular field analysis
Q91289731	Nonparametric chemical descriptors for the calculation of ligand-biopolymer affinities with machine-learning scoring functions
Q52382622	Novel algorithms for searching conformational space.
Q35026098	Novel anti-plasmodial hits identified by virtual screening of the ZINC database
Q51943955	Novel approach to evolutionary neural network based descriptor selection and QSAR model development.
Q58050992	Novel inhibitors to Taenia solium Cu/Zn superoxide dismutase identified by virtual screening
Q27670945	Novel isoquinolone PDK1 inhibitors discovered through fragment-based lead discovery
Q96819168	Novel phosphatidylinositol 4-kinases III beta (PI4KIIIβ) inhibitors discovered by virtual screening using free energy models
Q72393568	Nucleotide-binding properties of adenylate kinase from Escherichia coli: a molecular dynamics study in aqueous and vacuum environments
Q41874011	OVID and SUPER: Two overlap programs for drug design
Q30404061	Obituary: Corwin H. Hansch
Q45944054	Obituary: Toshio Fujita, QSAR pioneer.
Q50957370	Objective models for steroid binding sites of human globulins.
Q92137312	Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge
Q30485257	Of possible cheminformatics futures
Q43084203	On homology modeling of the M₂ muscarinic acetylcholine receptor subtype.
Q91934947	On the activation and deactivation pathways of the Lck kinase domain: a computational study
Q57278502	On the active site of mononuclear B1 metallo β-lactamases: a computational study
Q30844876	On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data
Q71347769	On the electrostatic and steric similarity of lactam compounds and the natural substrate for bacterial cell-wall biosynthesis
Q38971591	On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge
Q80865383	On the importance of topological descriptors in understanding structure-property relationships
Q46375027	On the interpretation and interpretability of quantitative structure-activity relationship models
Q73572205	On the molecular interaction between lactoferrin and the dye Red HE-3b. A novel approach for docking a charged and highly flexible molecule to protein surfaces
Q126276684	On the relevance of query definition in the performance of 3D ligand-based virtual screening
Q44485548	On the representation of electrostatic fields around ab initio charge distributions
Q52417243	On the suitability of semiempirical calculations as sources of force field parameters.
Q72593914	On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure
Q70233006	On the use of isovalued surfaces to determine molecule shape and reaction pathways
Q43979139	One site fits both: a model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme
Q28530221	Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information
Q51544926	Open3DALIGN: an open-source software aimed at unsupervised ligand alignment.
Q37522061	OpenCDLig: a free web application for sharing resources about cyclodextrin/ligand complexes.
Q53493142	Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.
Q42691078	Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges.
Q36116506	Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge
Q91248939	Optimisation of human VH domain antibodies specific to Mycobacterium tuberculosis heat shock protein (HSP16.3)
Q28264356	Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
Q43701183	Optimization of a mathematical topological pattern for the prediction of antihistaminic activity
Q28294267	Optimization of biaryl piperidine and 4-amino-2-biarylurea MCH1 receptor antagonists using QSAR modeling, classification techniques and virtual screening
Q37111553	Optimizing Dvl PDZ domain inhibitor by exploring chemical space.
Q36858968	Optimizing doped libraries by using genetic algorithms
Q67981520	Orientation and structure-building role of the water molecules bound at the contact surface of the dihydrofolate reductase-methotrexate complex
Q46841895	Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal
Q30363018	Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?
Q30360124	Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?
Q38818618	Overview of the SAMPL5 host-guest challenge: Are we doing better?
Q58556734	Overview of the SAMPL6 host-guest binding affinity prediction challenge
Q111149480	Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions
Q84129411	Overview of the perspectives devoted to tautomerism in molecular design
Q45897104	Oxygen-containing fragments in natural products
Q51500631	PAPQMD parametrization of molecular systems with cyclopropyl rings: conformational study of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid.
Q34584338	PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results
Q81055528	PLASS: protein-ligand affinity statistical score--a knowledge-based force-field model of interaction derived from the PDB
Q48474613	PLS modelling of structure-activity relationships of catechol O-methyltransferase inhibitors
Q36703753	PRO-LIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules
Q52346352	PRO-LIGAND: an approach to de novo molecular design. 3. A genetic algorithm for structure refinement.
Q48785859	PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules.
Q36763967	PROGEN: an automated modelling algorithm for the generation of complete protein structures from the alpha-carbon atomic coordinates
Q36682015	PRO_LIGAND: an approach to de novo molecular design. 4. Application to the design of peptides
Q36794957	PRO_LIGAND: an approach to de novo molecular design. 6. Flexible fitting in the design of peptides
Q36852276	PRO_SELECT: combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology
Q60194845	Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics
Q46345653	Parameterization of an empirical model for the prediction of n-octanol, alkane and cyclohexane/water as well as brain/blood partition coefficients
Q73041078	Parametrization of a force field for metals complexed to biomacromolecules: applications to Fe(II), Cu(II) and Pb(II)
Q39373257	Partition coefficients for the SAMPL5 challenge using transfer free energies.
Q52227962	Patenting computer-designed peptides.
Q45110662	Pattern recognition display methods for the analysis of computed molecular properties
Q69724835	Pattern recognition study of QSAR substituent descriptors
Q98647314	Pattern-free generation and quantum mechanical scoring of ring-chain tautomers
Q39301033	Pep-Calc.com: a set of web utilities for the calculation of peptide and peptoid properties and automatic mass spectral peak assignment
Q46016087	Peptide mimetics as enzyme inhibitors: use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor.
Q91063630	Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset
Q38613029	Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.
Q47797655	Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016.
Q46892685	Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies.
Q45110960	Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile
Q89949715	Performing solvation free energy calculations in LAMMPS using the decoupling approach
Q51937689	Permuting input for more effective sampling of 3D conformer space.
Q47796440	Peroxisome proliferator-activated receptors target family landscape: a chemometrical approach to ligand selectivity based on protein binding site analysis
Q67981523	Perspectives in QSAR: computer chemistry and pattern recognition
Q47796455	Pharmacophore and receptor models for neurokinin receptors
Q58748185	Pharmacophore development for antagonists at α1 adrenergic receptor subtypes
Q68121896	Pharmacophore identification by molecular modeling and chemometrics: the case of HMG-CoA reductase inhibitors
Q80260250	Pharmacophore model for bile acids recognition by the FPR receptor
Q57010606	Pharmacophore modeling and parallel screening for PPAR ligands
Q35395528	Pharmacophore modeling improves virtual screening for novel peroxisome proliferator-activated receptor-gamma ligands
Q74006401	Pharmacophore modelling of structurally unusual diltiazem mimics at L-type calcium channels
Q49177235	Pharmacophore refinement of gpIIb/IIIa antagonists based on comparative studies of antiadhesive cyclic and acyclic RGD peptides.
Q36124531	Pharmacophore-based virtual screening, biological evaluation and binding mode analysis of a novel protease-activated receptor 2 antagonist
Q33744181	Pharmacophore-driven identification of PPARγ agonists from natural sources.
Q97549635	Phenylalkylamines in calcium channels: computational analysis of experimental structures
Q48540899	Philip S. Magee: a life in QSAR.
Q43012038	Phosphorylation and ATP-binding induced conformational changes in the PrkC, Ser/Thr kinase from B. subtilis
Q52311354	Placement of medium-sized molecular fragments into active sites of proteins.
Q96349424	Plausible compounds drawn from plants as curative agents for neurodegeneration: An in-silico approach
Q39647348	Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test.
Q31023601	Possibilities for transfer of relevant data without revealing structural information
Q45942180	Possible allosteric interactions of monoindazole-substituted P2 cyclic urea analogues with wild-type and mutant HIV-1 protease.
Q48053795	Practical computational toolkits for dendrimers and dendrons structure design
Q43520105	Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1.
Q36268544	Predicting DPP-IV inhibitors with machine learning approaches.
Q80865387	Predicting allergic contact dermatitis: a hierarchical structure-activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors
Q43786256	Predicting anti-HIV activity: computational approach using a novel topological descriptor
Q44325902	Predicting anticonvulsant activity of benzamides/benzylamines: computational approach using topological descriptors
Q36645023	Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations
Q39310536	Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation.
Q90046659	Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0.
Q51477064	Predicting bioactive conformations and binding modes of macrocycles.
Q39449581	Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model
Q47679935	Predicting drug pharmacokinetic properties using molecular interaction fields and SIMCA.
Q47600233	Predicting drug-induced liver injury in human with Naïve Bayes classifier approach
Q34108242	Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models
Q84014403	Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations
Q34351290	Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4
Q48887633	Predicting hydration free energies with chemical accuracy: the SAMPL4 challenge.
Q79273419	Predicting infinite dilution activity coefficients of organic compounds in water by quantum-connectivity descriptors
Q57167810	Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge
Q52244281	Predicting nucleic acid torsion angle values using artificial neural networks.
Q89460097	Predicting octanol/water partition coefficients for the SAMPL6 challenge using the SM12, SM8, and SMD solvation models
Q92787012	Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields
Q91248938	Predicting protein-ligand binding modes for CELPP and GC3: workflows and insight
Q96349416	Predicting reactivity to drug metabolism: beyond P450s-modelling FMOs and UGTs
Q41616028	Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations
Q74336775	Predicting sequences and structures of MHC-binding peptides: a computational combinatorial approach
Q92006812	Predicting skin permeability using the 3D-RISM-KH theory based solvation energy descriptors for a diverse class of compounds
Q44608034	Predicting targets of compounds against neurological diseases using cheminformatic methodology.
Q47980758	Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study.
Q36590236	Predicting the effects of amino acid replacements in peptide hormones on their binding affinities for class B GPCRs and application to the design of secretin receptor antagonists
Q67976695	Predicting the product specificity and coupling of cytochrome P450cam
Q53185669	Predicting the relative binding affinity of mineralocorticoid receptor antagonists by density functional methods.
Q37549125	Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields
Q40775415	Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases
Q50978597	Prediction and interpretation of the lipophilicity of small peptides.
Q90797642	Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method
Q91347521	Prediction of P-glycoprotein inhibitors with machine learning classification models and 3D-RISM-KH theory based solvation energy descriptors
Q51709682	Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models.
Q36060565	Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).
Q34249481	Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields
Q87307951	Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics
Q28285760	Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs
Q47625069	Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.
Q48114822	Prediction of blood-brain barrier permeation using quantum chemically derived information
Q39122338	Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water
Q48054774	Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields.
Q31125942	Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field.
Q31117677	Prediction of cyclohexane-water distribution coefficients with COSMO-RS on the SAMPL5 data set.
Q34267386	Prediction of free energies of hydration with COSMO-RS on the SAMPL3 data set.
Q30732705	Prediction of free energies of hydration with COSMO-RS on the SAMPL4 data set.
Q58048746	Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field
Q30766874	Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field.
Q58048721	Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field
Q44882015	Prediction of in vitro metabolic stability of calcitriol analogs by QSAR.
Q51967777	Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme.
Q99637607	Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations
Q92787028	Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields
Q88917747	Prediction of partition and distribution coefficients in various solvent pairs with COSMO-RS
Q39394471	Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation
Q51960741	Prediction of plasma protein binding of drugs using Kier-Hall valence connectivity indices and 4D-fingerprint molecular similarity analyses.
Q37761334	Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
Q45965982	Prediction of standard Gibbs energies of the transfer of peptide anions from aqueous solution to nitrobenzene based on support vector machine and the heuristic method.
Q39887697	Prediction of tautomer ratios by embedded-cluster integral equation theory
Q45756379	Prediction of the binding mode of N2-phenylguanine derivative inhibitors to herpes simplex virus type 1 thymidine kinase
Q34662381	Prediction of the binding site of 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine in acetylcholinesterase by docking studies with the SYSDOC program
Q49177167	Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies.
Q91498593	Prediction of the n-octanol/water partition coefficients in the SAMPL6 blind challenge from MST continuum solvation calculations
Q70413433	Prediction of the three-dimensional structure of the enzymatic domain of t-PA
Q73315105	Prediction of the three-dimensional structure of the human Fas receptor by comparative molecular modeling
Q45966205	Prediction of the tissue/blood partition coefficients of organic compounds based on the molecular structure using least-squares support vector machines.
Q45739100	Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores
Q43114172	Predictions of hydration free energies from continuum solvent with solute polarizable models: the SAMPL2 blind challenge
Q44254255	Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection
Q38688678	Predictive cartography of metal binders using generative topographic mapping
Q96349427	Predictive potential of eigenvalue-based topological molecular descriptors
Q51966056	Preface to the special issue in memory of Phil Magee.
Q30995883	Presenting data in such a fashion that they can be used by other scientists
Q99610230	ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations
Q44201458	ProSeg: a database of local structures of protein segments.
Q85010731	Proceedings of the Third Annual Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) Challenge and Workshop. June 2009. Montreal, Canada
Q42860793	Prodrugs of aza nucleosides based on proton transfer reaction
Q30855791	Property distribution of drug-related chemical databases.
Q36092809	Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015.
Q39022371	Prospective virtual screening for novel p53-MDM2 inhibitors using ultrafast shape recognition
Q33241709	Protein Alpha Shape (PAS) Dock: a new gaussian-based score function suitable for docking in homology modelled protein structures
Q44490744	Protein Alpha Shape Similarity Analysis (PASSA): a new method for mapping protein binding sites. Application in the design of a selective inhibitor of tyrosine kinase 2.
Q45390949	Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr
Q44012277	Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
Q83139531	Protein farnesyltransferase: flexible docking studies on inhibitors using computational modeling
Q40775421	Protein fold recognition
Q40518742	Protein fragment reconstruction using various modeling techniques
Q62761925	Protein ligand docking based on empirical method for binding affinity estimation
Q50872388	Protein pocket and ligand shape comparison and its application in virtual screening.
Q32065414	Protein secondary structure templates derived from bioactive natural products. Combinatorial chemistry meets structure-based design
Q30351756	Protein structure prediction by tempering spatial constraints.
Q47655078	Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors
Q47382465	Protein-ligand docking using FFT based sampling: D3R case study
Q36788480	Protein-ligand docking with multiple flexible side chains
Q50051009	Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes.
Q91056148	Protein-small molecule docking with receptor flexibility in iMOLSDOCK
Q30349715	ProteinShop: a tool for interactive protein manipulation and steering.
Q57829621	Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3
Q39108153	Proteochemometric model for predicting the inhibition of penicillin-binding proteins
Q30400560	Proteus: a random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins
Q46628587	Protonation-induced stereoisomerism in nicotine: conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics
Q74006409	Pseudoreceptor model for ryanodine derivatives at calcium release channels
Q28292791	Public access to X-ray diffraction data
Q36718321	Pushing the boundaries of 3D-QSAR.
Q42281612	Pyridones as NNRTIs against HIV-1 mutants: 3D-QSAR and protein informatics
Q52033849	Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space.
Q54683502	QM/MM based 3D QSAR models for potent B-Raf inhibitors.
Q30392776	QMOD: physically meaningful QSAR
Q30358007	QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR.
Q40468021	QSAR and classification models of a novel series of COX-2 selective inhibitors: 1,5-diarylimidazoles based on support vector machines.
Q72803831	QSAR and conformational analysis of the antiinflammatory agent amfenac and analogues
Q104112873	QSAR and molecular docking for the search of AOX inhibitors: a rational drug discovery approach
Q33412179	QSAR application for the prediction of compound permeability with in silico descriptors in practical use.
Q30587124	QSAR model based on weighted MCS trees approach for the representation of molecule data sets
Q38857036	QSAR modeling and chemical space analysis of antimalarial compounds
Q81437670	QSAR modeling based on the bias/variance compromise: a harmonious and parsimonious approach
Q44587142	QSAR modeling of beta-lactam binding to human serum proteins
Q77763150	QSAR modeling with the electrotopological state indices: corticosteroids
Q28211747	QSAR of benzene derivatives: comparison of classical descriptors, quantum theoretic parameters and flip regression, exemplified by phenylalkylamine hallucinogens
Q67976701	QSAR of conformationally flexible molecules: comparative molecular field analysis of protein-tyrosine kinase inhibitors
Q44420537	QSAR of heterocyclic antifungal agents by flip regression
Q30985338	QSAR study and VolSurf characterization of anti-HIV quinolone library.
Q78249924	QSAR using 2D descriptors and TRIPOS' SIMCA
Q40218957	QSAR with experimental and predictive distributions: an information theoretic approach for assessing model quality
Q39835112	QSAR without arbitrary descriptors: the electron-conformational method
Q40800449	QSAR workbench: automating QSAR modeling to drive compound design
Q80480221	QSAR: dead or alive?
Q53539064	QSID Tool: a new three-dimensional QSAR environmental tool.
Q51093734	QSPR ensemble modelling of the 1:1 and 1:2 complexation of Co²⁺, Ni²⁺, and Cu²⁺ with organic ligands: relationships between stability constants.
Q51912723	QSPR modeling of UV absorption intensities.
Q52260139	QXP: powerful, rapid computer algorithms for structure-based drug design.
Q39896264	Qualitative prediction of blood-brain barrier permeability on a large and refined dataset
Q51892184	Quantitative Series Enrichment Analysis (QSEA): a novel procedure for 3D-QSAR analysis.
Q53551924	Quantitative measurement of protease ligand conformation.
Q51961345	Quantitative prediction of imprinting factor of molecularly imprinted polymers by artificial neural network.
Q46793452	Quantitative structure-activity relationship analysis of canonical inhibitors of serine proteases
Q46703800	Quantitative structure-activity relationship analysis of pyridinone HIV-1 reverse transcriptase inhibitors using the k nearest neighbor method and QSAR-based database mining
Q33774384	Quantitative structure-activity relationship analysis of β-amyloid aggregation inhibitors
Q46767212	Quantitative structure-activity relationship studies of mushroom tyrosinase inhibitors
Q73233699	Quantitative structure-activity relationships and comparative molecular field analysis of TIBO derivatised HIV-1 reverse transcriptase inhibitors
Q52373584	Quantitative structure-activity relationships by neural networks and inductive logic programming. I. The inhibition of dihydrofolate reductase by pyrimidines.
Q52373580	Quantitative structure-activity relationships by neural networks and inductive logic programming. II. The inhibition of dihydrofolate reductase by triazines.
Q51992732	Quantitative structure-activity relationships from optimised ab initio bond lengths: steroid binding affinity and antibacterial activity of nitrofuran derivatives.
Q50091251	Quantitative structure-activity relationships of mutagenic activity from quantum topological descriptors: triazenes and halogenated hydroxyfuranones (mutagen-X) derivatives.
Q71749035	Quantitative structure-agonist activity relationship of capsaicin analogues
Q89208049	Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose
Q58108987	Quantum chemical and molecular mechanics studies on the assessment of interactions between resveratrol and mutant SOD1 (G93A) protein
Q89460086	Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge
Q91291272	Quantum chemical studies on anion specificity of CαNN motif in functional proteins
Q44194554	Quantum chemical studies on tautomerism of barbituric acid in gas phase and in solution
Q67558776	Quantum chemical study on the interaction of some bisphosphonates and Ca2+: the role of molecular electrostatic potentials in the prediction of binding geometry
Q41931981	Quantum mechanical polar surface area
Q46445371	Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies
Q38950911	Quantum probability ranking principle for ligand-based virtual screening
Q107739603	Quantum simulations of SARS-CoV-2 main protease M enable high-quality scoring of diverse ligands
Q100739180	Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?
Q51359512	R-group template CoMFA combines benefits of "ad hoc" and topomer alignments using 3D-QSAR for lead optimization.
Q80651562	RIP MDL information systems. Is this really the beginning of a new era?
Q31062836	RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case
Q48335722	RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.
Q45950111	ROCS-derived features for virtual screening.
Q38647554	Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2.
Q57245415	Rapamycin: Biological and therapeutic effects, binding by immunophilins and molecular targets of action
Q39675574	Rapid activity prediction of HIV-1 integrase inhibitors: harnessing docking energetic components for empirical scoring by chemometric and artificial neural network approaches
Q33832248	Rapid discovery of inhibitors of Toxoplasma gondii using hybrid structure-based computational approach
Q44262192	Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge
Q91945283	Rational Design, synthesis and biological evaluation of novel triazole derivatives as potent and selective PRMT5 inhibitors with antitumor activity
Q92776270	Rational creation and systematic analysis of cervical cancer kinase-inhibitor binding profile
Q33873862	Rational design of an enzyme mutant for anti-cocaine therapeutics
Q38931722	Rational design of biaryl pharmacophore inserted noscapine derivatives as potent tubulin binding anticancer agents
Q72593889	Rational design of hirulog-type inhibitors of thrombin
Q72393577	Rational design of novel neurotensin mimetics: discovery of a pharmacologically unprecedented agent exhibiting concentration-dependent dual effects as antagonist and full agonist
Q84040958	Rational design, synthesis and biological evaluations of amino-noscapine: a high affinity tubulin-binding noscapinoid
Q31165909	Rational selection of training and test sets for the development of validated QSAR models
Q34133282	Rationalizing fragment based drug discovery for BACE1: insights from FB-QSAR, FB-QSSR, multi objective (MO-QSPR) and MIF studies.
Q98505048	ReSCoSS: a flexible quantum chemistry workflow identifying relevant solution conformers of drug-like molecules
Q30875868	Reactant- and product-based approaches to the design of combinatorial libraries
Q67891433	Reaction mechanisms in peptide synthesis. Part 1. Semiquantitative characteristics of the reactivity of 2-methyl-5(4H)-oxazolone with water and ammonia in the gas phase and weakly polar media
Q54071826	Reaction mechanisms in peptide synthesis. Part 2. Tautomerism of the peptide bond.
Q51400164	Real value prediction of protein folding rate change upon point mutation.
Q78683425	Recent advances in molecular diversity
Q107113685	Recent insights into cysteine protease specificity: Lessons for drug design
Q68494321	Receptor model for the molecular basis of tissue selectivity of 1, 4-dihydropyridine calcium channel drugs
Q58860167	Receptor-based 3D QSAR analysis of estrogen receptor ligands--merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods
Q28755020	Recommendations for evaluation of computational methods
Q73010965	Reconstruction of the 3D coordinates of alpha-carbon atoms of proteins from a pair of stereographic figures
Q78429536	Recovery of known T-cell epitopes by computational scanning of a viral genome
Q35841379	Refined homology model of monoacylglycerol lipase: toward a selective inhibitor
Q59188927	Refinement of Catalyst hypotheses using simplex optimisation
Q52081432	Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2.
Q48514606	Reflections on the past 25 years.
Q60194881	Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis candidate drug thioridazine with molecular simulations
Q47952018	Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP.
Q63916807	Relative binding orientations of adenosine A1 receptor ligands — A test case for Distributed Multipole Analysis in medicinal chemistry
Q44833190	Relative free energies of binding to thymidylate synthase of 2- and/or 4-thio and/or 5-fluoro analogues of dUMP.
Q43275587	Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length
Q48439266	Remembrances of Corwin Hansch.
Q71749022	Replacement of steric 6-12 potential-derived interaction energies by atom-based indicator variables in CoMFA leads to models of higher consistency
Q51390000	Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: rotational parameters of helices.
Q57460082	Representation of molecular structure using quantum topology with inductive logic programming in structure–activity relationships
Q44711419	Representation, searching and discovery of patterns of bases in complex RNA structures
Q74568406	Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools
Q90707908	Repurposing of known drugs for leishmaniasis treatment using bioinformatic predictions, in vitro validations and pharmacokinetic simulations
Q61999145	Rescoring of docking poses under Occam’s Razor: are there simpler solutions?
Q73803116	Research on anti-HIV-1 agents. Investigation on the CD4-Suradista binding mode through docking experiments
Q37588671	Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics.
Q112283807	RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology
Q91748155	Resveratrol as a nontoxic excipient stabilizes insulin in a bioactive hexameric form
Q42661891	Rethinking 3D-QSAR.
Q91978101	Revealing cytotoxic substructures in molecules using deep learning
Q48059059	Revealing the importance of linkers in K-series oxime reactivators for tabun-inhibited AChE using quantum chemical, docking and SMD studies.
Q48114689	Reverse engineering chemical structures from molecular descriptors: how many solutions?
Q81131521	Reverse-docking as a computational tool for the study of asymmetric organocatalysis
Q95276292	Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy
Q52230459	RigFit: a new approach to superimposing ligand molecules.
Q50627884	Ring system-based chemical graph generation for de novo molecular design.
Q45963765	Robust optimization of scoring functions for a target class.
Q40513178	Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study
Q86504064	Role of indirect readout mechanism in TATA box binding protein-DNA interaction
Q81944524	Role of protein flexibility in the design of Bcl-X(L) targeting agents: insight from molecular dynamics
Q88564664	Role of protein structure and the role of individual fingers in zinc finger protein-DNA recognition: a molecular dynamics simulation study and free energy calculations
Q73194561	Role of tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase
Q43107625	SAMPL2 and continuum modeling
Q84121860	SAMPL2 challenge: prediction of solvation energies and tautomer ratios
Q59795479	SAMPL3: blinded prediction of host–guest binding affinities, hydration free energies, and trypsin inhibitors
Q37735497	SAMPL4 & DOCK3.7: lessons for automated docking procedures
Q45204541	SAMPL4, a blind challenge for computational solvation free energies: the compounds considered
Q45975662	SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling.
Q92787006	SAMPL6 Octanol-water partition coefficients from alchemical free energy calculations with MBIS atomic charges
Q90785851	SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches
Q57463683	SAMPL6 challenge results from [Formula: see text] predictions based on a general Gaussian process model
Q92892921	SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations
Q56342046	SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach
Q91500741	SAMPL6 host-guest challenge: binding free energies via a multistep approach
Q89460093	SAMPL6 logP challenge: machine learning and quantum mechanical approaches
Q58048679	SAMPL6: calculation of macroscopic pKa values from ab initio quantum mechanical free energies
Q100512762	SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations
Q98293823	SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations
Q101325799	SAMPL7: Host-guest binding prediction by molecular dynamics and quantum mechanics
Q58225487	SCF-MO study of the polyglycine II structure
Q32058654	SLATE: a method for the superposition of flexible ligands.
Q51650890	SMART: a solvent-accessible triangulated surface generator for molecular graphics and boundary element applications.
Q61960988	SPROUT, HIPPO and CAESA: Tools for de novo structure generation and estimation of synthetic accessibility
Q52398734	SPROUT: a program for structure generation.
Q72741870	Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA
Q44833188	Sampling and convergence in free energy calculations of protein-ligand interactions: the binding of triphenoxypyridine derivatives to factor Xa and trypsin
Q92269008	Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4
Q52321857	Sampling conformational hyperspace: techniques for improving completeness.
Q45722871	Scaffold mining of kinase hinge binders in crystal structure database
Q28654727	Scientific and technical data sharing: a trading perspective
Q24621331	Scientific workflow systems: Pipeline Pilot and KNIME
Q37288619	Scoring confidence index: statistical evaluation of ligand binding mode predictions
Q36289042	Scoring functions--the first 100 years.
Q74633107	Scoring functions: a view from the bench
Q71851460	Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities
Q81055524	Scoring protein-protein docked structures based on the balance and tightness of binding
Q33530648	Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model
Q32060283	Screening the molecular surface of human anticoagulant protein C: a search for interaction sites
Q33475687	Second-generation de novo design: a view from a medicinal chemist perspective
Q31015468	Secure analysis of distributed chemical databases without data integration
Q57976083	Seeing our way to drug design
Q85723134	Seeking potential anticonvulsant agents that target GABAA receptors using experimental and theoretical procedures
Q78057587	Selective assembly of cyclodextrins on poly(ethylene oxide)-poly(propylene oxide) block copolymers
Q43631520	Selective inhibition of 6-phosphogluconate dehydrogenase from Trypanosoma brucei.
Q74006420	Selectivity analysis of 5-(arylthio)-2,4-diaminoquinazolines as inhibitors of Candida albicans dihydrofolate reductase by molecular dynamics simulations
Q82059180	Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity
Q46558730	Semi-rigid analogues of the calcium antagonist verapamil: a molecular modelling study
Q30333072	Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase.
Q91834657	Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches
Q48082192	Shape information from a critical point analysis of calculated electron density maps: application to DNA-drug systems
Q90797777	Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3
Q41961153	Shaping suvorexant: application of experimental and theoretical methods for driving synthetic designs
Q68049862	Shell Conference on Computer-Aided Molecular Modelling. October 4-6, 1987, Hoenderloo, The Netherlands
Q83841243	Sialyldisaccharide conformations: a molecular dynamics perspective
Q48055229	Side chain flexibility and the pore dimensions in the GABAA receptor.
Q96349420	Side chain virtual screening of matched molecular pairs: a PDB-wide and ChEMBL-wide analysis
Q33374550	Side-chain conformational space analysis (SCSA): a multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities
Q92164230	Significantly different effects of tetrahydroberberrubine enantiomers on dopamine D1/D2 receptors revealed by experimental study and integrated in silico simulation
Q82908722	Silver threads
Q56835065	Similarity and Dissimilarity: A Medicinal Chemist's View
Q30424998	Similarity and complementarity of molecular shapes: applicability of a topological analysis approach
Q44490734	Similarity based SAR (SIBAR) as tool for early ADME profiling
Q44684389	Similarity of molecular shape
Q30890613	Similarity screening of molecular data sets
Q52273177	Similarity searching in files of three-dimensional chemical structures: representation and searching of molecular electrostatic potentials using field-graphs.
Q43701172	Similarity searching in large combinatorial chemistry spaces
Q57012717	Similarity versus docking in 3D virtual screening
Q56917067	Similarity-based descriptors (SIBAR) – A tool for safe exchange of chemical information?
Q73331725	Simple knowledge-based descriptors to predict protein-ligand interactions. methodology and validation
Q96158677	Simplified activity cliff network representations with high interpretability and immediate access to SAR information
Q71749025	Simulation analysis of formycin 5'-monophosphate analog substrates in the ricin A-chain active site
Q91538138	Simulation of MDM2 N-terminal domain conformational lability in the presence of imidazoline based inhibitors of MDM2-p53 protein-protein interaction
Q38302869	Simulation of carbohydrate-protein interactions: computer-aided design of a second generation GM1 mimic.
Q33323615	Simulation-based cheminformatic analysis of organelle-targeted molecules: lysosomotropic monobasic amines
Q43805832	Simultaneous prediction of aqueous solubility and octanol/water partition coefficient based on descriptors derived from molecular structure
Q41905100	Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions
Q43111257	Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach.
Q40412571	Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling
Q47240999	Size-intensive descriptors
Q30577535	Small molecule correctors of F508del-CFTR discovered by structure-based virtual screening
Q43000482	So you think you understand tautomerism?
Q92389169	Software to obtain spatially localized functions from different radial functions
Q71483796	Solution conformation by NMR and molecular modeling of three sulfide-free somatostatin octapeptide analogs compared to angiopeptin
Q43730054	Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models.
Q57975330	Solvation of the active site of cytochrome P450-cam
Q45002483	Solvent effect on the synthesis of clarithromycin: a molecular dynamics study
Q42649305	Solvent effects on dimeric self-association of 2-pyrrolidinone: an ab initio study
Q57829045	Some conclusions regarding the predictions of tautomeric equilibria in solution based on the SAMPL2 challenge
Q51482694	Some findings relevant to the mechanistic interpretation in the case of predictive models for carcinogenicity based on the counter propagation artificial neural network.
Q57009135	Some thoughts on the “A” in computer-aided molecular design
Q91480966	Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase
Q49993604	Sparse QSAR modelling methods for therapeutic and regenerative medicine.
Q40145049	Spatial chemical distance based on atomic property fields
Q83762002	Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study
Q89690113	Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states
Q46902419	Statistical analyses and computational prediction of helical kinks in membrane proteins
Q36568029	Statistical analysis of EGFR structures' performance in virtual screening
Q41432276	Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding.
Q30843844	Statistical relationships among docking scores for different protein binding sites
Q57907612	Statistical variation in progressive scrambling
Q89032540	Statistics in molecular modeling: a summary
Q72803827	Stereochemistry of charged nitrogen-aromatic interactions and its involvement in ligand-receptor binding
Q36761310	Stereochemistry of ulapualides, a new family of tris-oxazole-containing macrolide ionophores from marine nudibranchs. A molecular mechanics study
Q73013874	Steroid binding by antibodies and artificial receptors: exploration of theoretical methods to determine the origins of binding affinities and specificities
Q50149089	Strategic approaches to drug design. I. An integrated software framework for molecular modelling.
Q69843559	Strategic approaches to drug design. II. Modelling studies on phosphodiesterase substrates and inhibitors
Q56040349	Strategies I
Q68844987	Strategies II
Q68049867	Strategies for modelling of catalysts
Q38558154	Strategies for the determination of pharmacophoric 3D database queries
Q79489038	Strategies to design pyrazolyl urea derivatives for p38 kinase inhibition: a molecular modeling study
Q91777930	Structural analysis of the Aβ(11-42) amyloid fibril based on hydrophobicity distribution
Q73803111	Structural analysis of the KGD sequence loop of barbourin, an alphaIIbbeta3-specific disintegrin
Q43021660	Structural and functional analysis of a novel psychrophilic β-mannanase from Glaciozyma antarctica PI12.
Q67520713	Structural changes by sulfoxidation of phenothiazine drugs
Q90445530	Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1)
Q71657322	Structural comparison of NK2 receptor agonists and antagonists
Q30009248	Structural dynamics of native and V260E mutant C-terminal domain of HIV-1 integrase
Q60470924	Structural evaluation of an alternative Protein A biomimetic ligand for antibody purification
Q93383637	Structural explanation for the tunable substrate specificity of an E. coli nucleoside hydrolase: insights from molecular dynamics simulations
Q46647594	Structural functionality, catalytic mechanism modeling and molecular allergenicity of phenylcoumaran benzylic ether reductase, an olive pollen (Ole e 12) allergen
Q34068107	Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening
Q38673001	Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis
Q61697352	Structural insights for the design of new PPARgamma partial agonists with high binding affinity and low transactivation activity
Q35228394	Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2.
Q39469790	Structural insights into the mechanism of translational inhibition by the fungicide sordarin
Q36168250	Structural insights into transient receptor potential vanilloid type 1 (TRPV1) from homology modeling, flexible docking, and mutational studies
Q35950237	Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold
Q52445252	Structural investigations and modeling of cavities in clathrates
Q46457886	Structural modeling of glucanase-substrate complexes suggests a conserved tyrosine is involved in carbohydrate recognition in plant 1,3-1,4-beta-D-glucanases
Q33455932	Structural models in the assessment of protein druggability based on HTS data
Q38550766	Structural models of antibody variable fragments: a method for investigating binding mechanisms
Q33698990	Structural organization of G-protein-coupled receptors
Q43600959	Structural pairwise comparisons of HLM stability of phenyl derivatives: Introduction of the Pfizer metabolism index (PMI) and metabolism-lipophilicity efficiency (MLE).
Q43015827	Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function
Q47813312	Structural rationale for the cross-resistance of tumor cells bearing the A399V variant of elongation factor eEF1A1 to the structurally unrelated didemnin B, ternatin, nannocystin A and ansatrienin B.
Q34525694	Structural requirements of Na+-dependent antidopaminergic agents: Tropapride, Piquindone, Zetidoline, and Metoclopramide. Comparison with Na+-independent ligands
Q50044099	Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport.
Q47361820	Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.
Q79759895	Structure and reaction based evaluation of synthetic accessibility
Q41022676	Structure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP.
Q91843408	Structure based design of selective SHP2 inhibitors by De novo design, synthesis and biological evaluation
Q71870821	Structure determination of a tetradecapeptide mimicking the RXVRG consensus sequence recognized by a Xenopus laevis skin endoprotease: an approach based on simulated annealing and 1H NMR
Q71483765	Structure of a cyclic peptide with a catalytic triad, determined by computer simulation and NMR spectroscopy
Q71347767	Structure-activity analysis of fluorinated 1-N-arylamino-1-arylmethanephosphonic acid esters as inhibitors of the NADH:ubiquinone oxidoreductase (complex I)
Q71347776	Structure-activity correlation study of HIV-1 inhibitors: electronic and molecular parameters
Q67509932	Structure-activity relationship between the 3D distribution of the electrophilicity of sugar derivatives and their cytotoxic and antiviral properties
Q60546558	Structure-activity relationship of Ca2+ channel blockers: A study using conformational analysis and chemometric methods
Q33230213	Structure-activity relationships for a new family of sulfonylurea herbicides
Q68843235	Structure-activity relationships for apomorphine congeners. Conformational energies vs. biological activities
Q73604203	Structure-activity relationships of cannabinoids: a joint CoMFA and pseudoreceptor modelling study
Q39790677	Structure-activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations
Q52444142	Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation.
Q51029309	Structure-activity relationships of thiostrepton derivatives: implications for rational drug design.
Q38348110	Structure-affinity relationships for the binding of actinomycin D to DNA.
Q43631515	Structure-based 3D QSAR and design of novel acetylcholinesterase inhibitors
Q46380009	Structure-based CoMFA and CoMSIA study of indolinone inhibitors of PDK1.
Q44371167	Structure-based QSAR study on differential inhibition of human prostaglandin endoperoxide H synthase-2 (COX-2) by nonsteroidal anti-inflammatory drugs.
Q36134510	Structure-based approach for identification of novel phenylboronic acids as serine-β-lactamase inhibitors.
Q31101083	Structure-based combinatorial library design: discovery of non-peptidic inhibitors of caspases 3 and 8.
Q46522604	Structure-based design of Aurora A & B inhibitors.
Q46732054	Structure-based design of ligands for protein basic domains: application to the HIV-1 Tat protein
Q34270442	Structure-based design of oxygen-linked macrocyclic kinase inhibitors: discovery of SB1518 and SB1578, potent inhibitors of Janus kinase 2 (JAK2) and Fms-like tyrosine kinase-3 (FLT3).
Q74006396	Structure-based design of potent CDK1 inhibitors derived from olomoucine
Q35158312	Structure-based design, synthesis and biological evaluation of β-glucuronidase inhibitors.
Q48023914	Structure-based drug design, synthesis and biological assays of P. falciparum Atg3-Atg8 protein-protein interaction inhibitors.
Q30420492	Structure-based identification and clustering of protein families and superfamilies
Q30330267	Structure-based ligand design for flexible proteins: application of new F-DycoBlock.
Q44711412	Structure-based prediction of free energy changes of binding of PTP1B inhibitors
Q34380036	Structure-based virtual screening of small-molecule antagonists of platelet integrin αIIbβ3 that do not prime the receptor to bind ligand
Q40333119	Structure-guided fragment-based in silico drug design of dengue protease inhibitors.
Q35103542	Structure-guided optimization of small molecule c-Abl activators
Q48332149	Structure-reactivity modeling using mixture-based representation of chemical reactions.
Q53401303	Structure-toxicity relationships of polycyclic aromatic hydrocarbons using molecular quantum similarity.
Q43293597	Studies of chirality effect of 4-(phenylamino)-pyrrolo[2,1-f][1,2,4]triazine on p38alpha by molecular dynamics simulations and free energy calculations
Q39671594	Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function
Q60860104	Substrate binding to mammalian 15-lipoxygenase
Q45903781	Substrate recognition by norovirus polymerase: microsecond molecular dynamics study.
Q54376746	Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures
Q34249453	Substructure and whole molecule approaches for calculating log P.
Q34413555	Subunit rotation models activation of serotonin 5-HT3AB receptors by agonists
Q51699038	Successful identification of key chemical structure modifications that lead to improved ADME profiles.
Q40634123	Superimposition evaluation of ecdysteroid agonist chemotypes through multidimensional QSAR.
Q100995310	Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein
Q51918959	Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds.
Q67475420	Surface comparisons of some odour molecules: Conformational calculations on sandalwood odour V
Q46358770	Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
Q36098724	Surflex-Dock: Docking benchmarks and real-world application
Q31015460	Surrogate data--a secure way to share corporate data
Q33227352	Surrogate docking: structure-based virtual screening at high throughput speed
Q67971693	Symposium overview. Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water
Q39567997	Symposium overview. The Shell Conference on Computer-Aided Molecular Modelling
Q30425177	Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly]
Q30564569	Systematic assessment of scaffold distances in ChEMBL: prioritization of compound data sets for scaffold hopping analysis in virtual screening
Q92642794	Systematic computational identification of promiscuity cliff pathways formed by inhibitors of the human kinome
Q87307728	Systematic mining of analog series with related core structures in multi-target activity space
Q34130507	T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles
Q47703604	TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers
Q38450152	TOPS-MODE versus DRAGON descriptors to predict permeability coefficients through low-density polyethylene
Q51939563	TRAJELIX: a computational tool for the geometric characterization of protein helices during molecular dynamics simulations.
Q30988299	Tales from the war on error: the art and science of curating QSAR data
Q112712975	Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking
Q90374510	TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree
Q36014246	TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models
Q77428763	Tautomeric equilibria in 8-oxopurines: implications for mutagenicity
Q39885239	Tautomerism in chemical information management systems
Q84274723	Tautomerism in drug discovery
Q33918117	Tautomerism in large databases
Q73010959	Tautomerism of xanthine and alloxanthine: a model for substrate recognition by xanthine oxidase
Q51713084	Tautomerism, Hammett sigma, and QSAR.
Q43683239	Tautomers and reference 3D-structures: the orphans of in silico drug design
Q83816713	Tautomers and topomers: challenging the uncertainties of direct physicochemical modeling
Q44282349	Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances
Q87963470	Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs
Q51118133	Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies.
Q87184813	Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge
Q46006136	Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test.
Q46720955	The 3D structure of the binding pocket of the human oxytocin receptor for benzoxazine antagonists, determined by molecular docking, scoring functions and 3D-QSAR methods
Q27676336	The DINGO dataset: a comprehensive set of data for the SAMPL challenge
Q69386533	The Gold Rush of '89
Q30832654	The IUPAC aqueous and non-aqueous experimental pKa data repositories of organic acids and bases
Q48545009	The Journal of Computer-Aided Molecular Design: a bibliometric note.
Q28654725	The Protein Data Bank archive as an open data resource
Q30840331	The Royal Society of Chemistry and the delivery of chemistry data repositories for the community
Q51145300	The SAMPL2 blind prediction challenge: introduction and overview.
Q83811405	The SAMPL3 blind prediction challenge: transfer energy overview
Q33740864	The SAMPL4 host-guest blind prediction challenge: an overview.
Q39113611	The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations
Q38828454	The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous pK a, and cyclohexane-water log D.
Q39379522	The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method
Q92956891	The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations
Q90729516	The SAMPL6 challenge on predicting aqueous pKa values from EC-RISM theory
Q92934486	The SAMPL6 challenge on predicting octanol-water partition coefficients from EC-RISM theory
Q69843556	The active analog approach applied to the pharmacophore identification of benzodiazepine receptor ligands
Q84373290	The advent and evolution of QSAR at Pomona College
Q71851466	The agonistic binding site at the histamine H2 receptor. I. Theoretical investigations of histamine binding to an oligopeptide mimicking a part of the fifth transmembrane alpha-helix
Q71851470	The agonistic binding site at the histamine H2 receptor. II. Theoretical investigations of histamine binding to receptor models of the seven alpha-helical transmembrane domain
Q53119806	The analysis of the market success of FDA approvals by probing top 100 bestselling drugs.
Q46164687	The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors
Q70790879	The atom assignment problem in automated de novo drug design. 1. Transferability of molecular fragment properties
Q52334003	The atom assignment problem in automated de novo drug design. 2. A method for molecular graph and fragment perception.
Q52333998	The atom assignment problem in automated de novo drug design. 3. Algorithms for optimization of fragment placement onto 3D molecular graphs.
Q52327717	The atom assignment problem in automated de novo drug design. 4. Tests for site-directed fragment placement based on molecular complementarity.
Q70984344	The atom assignment problem in automated de novo drug design. 5. Tests for envelope-directed fragment placement based on molecular similarity
Q91846661	The backbone of our chemical computations
Q42636964	The big problems don't go away by themselves
Q33228624	The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets
Q30977737	The challenges of making decisions using uncertain data
Q39674506	The character of molecular modeling
Q30051305	The chirality problem in P-substituted oligonucleotides
Q52289439	The comparison of geometric and electronic properties of molecular surfaces by neural networks: application to the analysis of corticosteroid-binding globulin activity of steroids.
Q68012970	The computational design of test compounds with potentially specific biological activity: histamine-H2 agonists derived from 5-HT/H2 antagonists
Q33214112	The computer program LUDI: a new method for the de novo design of enzyme inhibitors
Q46862343	The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA.
Q52066527	The configurational dependence of binding free energies: a Poisson-Boltzmann study of Neuraminidase inhibitors.
Q68665070	The conformational preferences of gamma-lactam and its role in constraining peptide structure
Q48020849	The consequences of translational and rotational entropy lost by small molecules on binding to proteins
Q45959177	The continuous molecular fields approach to building 3D-QSAR models.
Q71347782	The coordination of the catalytic zinc in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations
Q101240285	The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design
Q46630851	The de novo design of median molecules within a property range of interest
Q34326042	The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
Q52247866	The discovery of indicator variables for QSAR using inductive logic programming.
Q67865142	The discovery of novel auxin transport inhibitors by molecular modeling and three-dimensional pattern analysis
Q69601247	The educational foundation of Computational Chemistry
Q83949384	The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine-thymine and guanine-cytosine base pairs
Q73652657	The effect of isodensity surface sampling on ESP derived charges and the effect of adding bondcenters on DMA derived charges
Q48592247	The effect of numerical error on the reproducibility of molecular geometry optimizations.
Q45087562	The effect of physical organic properties on hydrophobic fields
Q45002480	The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models.
Q46666631	The effects of characteristics of substituents on toxicity of the nitroaromatics: HiT QSAR study
Q43084564	The effects of tautomerism on the nature of molecules in the solid state
Q39664353	The errors of our ways: taking account of error in computer-aided drug design to build confidence intervals for our next 25 years
Q30395547	The evolution of drug design at Merck Research Laboratories
Q34241696	The future of molecular dynamics simulations in drug discovery
Q41830975	The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures.
Q39671847	The great descriptor melting pot: mixing descriptors for the common good of QSAR models
Q67649805	The histamine H1-receptor antagonist binding site. Part I: Active conformation of cyproheptadine
Q54964899	The immunophilins
Q30997856	The impact of data integrity on decision making in early lead discovery
Q52098154	The implementation of ab initio quantum chemistry calculations on transporters.
Q35016524	The importance of molecular complexity in the design of screening libraries.
Q48055147	The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.
Q30421420	The importance of short structural motifs in protein structure analysis
Q70233002	The inclusion of electrostatic hydration energies in molecular mechanics calculations
Q39681298	The inevitable QSAR renaissance
Q89448145	The influence of hydrogen bonding on partition coefficients
Q72240650	The matching of electrostatic extrema: a useful method in drug design? A study of phosphodiesterase III inhibitors
Q31963506	The measurement of molecular diversity by receptor site interaction simulation
Q36843694	The measurement of molecular diversity: a three-dimensional approach
Q39568009	The modelling of nucleophilic and electrophilic additions to organometallic complexes using molecular graphics techniques
Q39794961	The molecular mechanism studies of chirality effect of PHA-739358 on Aurora kinase A by molecular dynamics simulation and free energy calculations
Q44342941	The mu- and delta-opioid pharmacophore conformations of cyclic beta-casomorphin analogues indicate docking of the Phe3 residue to different domains of the opioid receptors
Q33464348	The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design
Q33469695	The multiple roles of computational chemistry in fragment-based drug design
Q44587151	The nature of topological parameters. I. Are topological parameters 'fundamental properties'?
Q47622456	The nature of topological parameters. II. The composition of topological parameters
Q39084836	The need for scientific software engineering in the pharmaceutical industry
Q73913489	The orientation of N-H...O=C and N-H...N hydrogen bonds in biological systems: how good is a point charge as a model for a hydrogen bonding atom?
Q39676663	The perspectives of computational chemistry modeling
Q45966344	The prediction of human oral absorption for diffusion rate-limited drugs based on heuristic method and support vector machine.
Q34648848	The probable conformation of substrates recognized by dipeptidyl-peptidase IV and some aspects of the catalytic mechanism derived from theoretical investigations
Q84966543	The receptor-dependent LQTA-QSAR: application to a set of trypanothione reductase inhibitors
Q77763162	The reconstruction of atomic co-ordinates from a protein stereo ribbon diagram when additional information for sufficient sidechain positions is available
Q51555075	The reductionist paradox: are the laws of chemistry and physics sufficient for the discovery of new drugs?
Q92829701	The role of human in the loop: lessons from D3R challenge 4
Q91108678	The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations
Q90203330	The role of water and protein flexibility in the structure-based virtual screening of allosteric GPCR modulators: an mGlu5 receptor case study
Q57235382	The search for a new model structure of beta-factor XIIa
Q73233694	The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase
Q56904259	The sequence homologies of cytochromes P-450 and active-site geometries
Q83972920	The state of the guanosine nucleotide allosterically affects the interfaces of tubulin in protofilament
Q40415316	The statistics of virtual screening and lead optimization
Q77365350	The structural and electronical factors that contribute affinity for the time-dependent inhibition of PGHS-1 by indomethacin, diclofenac and fenamates
Q67822565	The structure-activity relationship of inhibitors of serotonin uptake and receptor binding
Q52395210	The use of an algorithmic method for small molecule superimpositions in the design of antiviral agents.
Q51103643	The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators.
Q43993646	The veil of commercialism
Q58005877	The voltage-gated potassium channel: Sequence analysis and molecular modelling of the pore domain
Q59614151	Theoretical descriptors for the quantitative rationalisation of plastocyanin mutant functional propertiess
Q59614218	Theoretical investigation of substrate specificity for cytochromes P450 IA2, P450 IID6 and P450 IIIA4
Q68079169	Theoretical models for the conformations and the protonation of triacetonamine
Q89414557	Theoretical models to predict the inhibitory effect of ligands of sphingosine kinase 1 using QTAIM calculations and hydrogen bond dynamic propensity analysis
Q69386532	Theoretical studies of the mechanism of the action of the neurohypophyseal hormones. I. Molecular electrostatic potential (MEP) and molecular electrostatic field (MEF) maps of some vasopressin analogues
Q50473551	Theoretical studies on effective metal-to-ligand charge transfer characteristics of novel ruthenium dyes for dye sensitized solar cells.
Q34024760	Theoretical studies on the interaction of partial agonists with the 5-HT2A receptor
Q53736952	Theoretical studies on the reaction of mono- and ditriflate derivatives of 1,4:3,6-dianhydro-D-mannitol with trimethylamine--Can a quaternary ammonium salt be a source of the methyl group?
Q44896304	Theoretical study of selective methylation in the synthesis of azithromycin
Q43605230	Thermodynamic aspects of hydrophobicity and biological QSAR.
Q44835970	Thermodynamic conformational analysis and structural stability of the nicotinic analgesic ABT-594.
Q68843238	Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry
Q33961846	Thermodynamic integration to predict host-guest binding affinities
Q27702163	Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data
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Q30356850	Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors.
Q38559642	Three-dimensional hydrogen-bond geometry and probability information from a crystal survey
Q42547091	Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ.
Q45184582	Three-dimensional quantitative structure-activity and structure-selectivity relationships of dihydrofolate reductase inhibitors.
Q46865333	Three-dimensional quantitative structure-activity relationship (3D QSAR) and pharmacophore elucidation of tetrahydropyran derivatives as serotonin and norepinephrine transporter inhibitors.
Q38562048	Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors
Q41387262	Time dependent analysis of assay comparability: a novel approach to understand intra- and inter-site variability over time.
Q51648149	Time-efficient flexible superposition of medium-sized molecules.
Q92164237	ToGo-WF: prediction of RNA tertiary structures and RNA-RNA/protein interactions using the KNIME workflow
Q56985255	Tomocomd-Cardd, a novel approach for computer-aided ? rational? drug design: I. Theoretical and experimental assessment of a promising method for computational screening and in silico design of new anthelmintic compounds
Q48260317	Tools, techniques, organisation and culture of the CADD group at Sygnature Discovery
Q51958833	Topological side-chain classification of beta-turns: ideal motifs for peptidomimetic development.
Q89036698	Touching proteins with virtual bare hands : Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware
Q81305424	Toward Mycobacterium tuberculosis DXR inhibitor design: homology modeling and molecular dynamics simulations
Q51637459	Toward better QSAR/QSPR modeling: simultaneous outlier detection and variable selection using distribution of model features.
Q39331916	Toward the discovery of inhibitors of babesipain-1, a Babesia bigemina cysteine protease: in vitro evaluation, homology modeling and molecular docking studies
Q77428758	Toward the identification of the cardiac cGMP inhibited-phosphodiesterase catalytic site
Q35029376	Towards a new age of virtual ADME/TOX and multidimensional drug discovery
Q52897990	Towards a rational spacer design for bivalent inhibition of estrogen receptor.
Q52462682	Towards an identification of the pyrethroid pharmacophore. A molecular modelling study of some pyrethroid esters.
Q71699021	Towards an understanding of the molecular basis of hydrophobicity
Q80082282	Towards discovering dual functional inhibitors against both wild type and K103N mutant HIV-1 reverse transcriptases: molecular docking and QSAR studies on 4,1-benzoxazepinone analogues
Q36827832	Towards the automatic design of synthetically accessible protein ligands: peptides, amides and peptidomimetics
Q51967888	Towards the chemometric dissection of peptide--HLA-A*0201 binding affinity: comparison of local and global QSAR models.
Q45940902	Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution.
Q89724281	Towards the understanding of the activity of G9a inhibitors: an activity landscape and molecular modeling approach
Q39841282	Trainable structure-activity relationship model for virtual screening of CYP3A4 inhibition.
Q44207658	Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.
Q52473279	Triangulation algorithms for the representation of molecular surface properties.
Q36328661	Triple hydrogen bonding in a circular arrangement: ab initio, DFT and first-principles MD studies of tris-hydroxyaryl enamines
Q33273270	TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time
Q45232748	Tuning of hydrogen bond strength using substituents on phenol and aniline: a possible ligand design strategy
Q50921495	Two-track virtual screening approach to identify both competitive and allosteric inhibitors of human small C-terminal domain phosphatase 1.
Q33271049	Ultrafast de novo docking combining pharmacophores and combinatorics
Q30379556	Ultrafast protein structure-based virtual screening with Panther.
Q90857877	Uncovering abnormal changes in logP after fluorination using molecular dynamics simulations
Q91480971	Undersampling: case studies of flaviviral inhibitory activities
Q53663557	Understanding and modulating cyclin-dependent kinase inhibitor specificity: molecular modeling and biochemical evaluation of pyrazolopyrimidinones as CDK2/cyclin A and CDK4/cyclin D1 inhibitors.
Q51913215	Understanding hERG inhibition with QSAR models based on a one-dimensional molecular representation.
Q51580291	Understanding molecular structure from molecular mechanics.
Q46456237	Understanding the mechanism of cellulose dissolution in 1-butyl-3-methylimidazolium chloride ionic liquid via quantum chemistry calculations and molecular dynamics simulations
Q84230612	Understanding the molecular interactions of different radical scavengers with ribonucleotide reductase M2 (hRRM2) domain: opening the gates and gaining access
Q61644525	Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations
Q92452767	Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule
Q57012683	Unsupervised guided docking of covalently bound ligands
Q39784558	Upperbound procedures for the identification of similar three-dimensional chemical structures
Q50790893	Urgency and austerity as drivers of success.
Q62511444	Use of electron-electron repulsion energy as a molecular descriptor in QSAR and QSPR studies
Q91347516	Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge
Q30328519	Use of surface area computations to describe atom-atom interactions.
Q52885309	Use of the hydrogen bond potential function in a comparative molecular field analysis (CoMFA) on a set of benzodiazepines.
Q43892219	Using a homology model of cytochrome P450 2D6 to predict substrate site of metabolism
Q79761837	Using a pharmacophore representation concept to elucidate molecular similarity of dopamine antagonists
Q46457884	Using a staged multi-objective optimization approach to find selective pharmacophore models
Q115732707	Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction
Q47301557	Using halogen bonds to address the protein backbone: a systematic evaluation
Q47622439	Using particle swarms for the development of QSAR models based on K-nearest neighbor and kernel regression
Q47614697	Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2.
Q58614302	Using steered molecular dynamics to study the interaction between ADP and the nucleotide-binding domain of yeast Hsp70 protein Ssa1
Q31147061	Utilizing high throughput screening data for predictive toxicology models: protocols and application to MLSCN assays
Q27136493	VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
Q56749500	VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface
Q33378588	VSDMIP: virtual screening data management on an integrated platform.
Q46819561	Validated ligand mapping of ACE active site
Q92787024	Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction
Q31112340	Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock
Q47863372	Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of D-amino acid oxidase inhibitors
Q64168637	Validation tools for variable subset regression
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Q45281821	Variable selection and model validation of 2D and 3D molecular descriptors
Q30983470	Variable selection and specification of robust QSAR models from multicollinear data: arylpiperazinyl derivatives with affinity and selectivity for alpha2-adrenoceptors
Q40715107	Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches
Q43605232	Very empirical treatment of solvation and entropy: a force field derived from log Po/w
Q56897201	Viral cysteine proteinases
Q27136404	Virtual Computational Chemistry Laboratory – Design and Description
Q50550611	Virtual and experimental high-throughput screening (HTS) in search of novel inosine 5'-monophosphate dehydrogenase II (IMPDH II) inhibitors.
Q30864246	Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide
Q34368348	Virtual fragment screening: exploration of MM-PBSA re-scoring
Q51900328	Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios.
Q34065423	Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge
Q42241501	Virtual screening of the SAMPL4 blinded HIV integrase inhibitors dataset.
Q34243088	Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK.
Q40578605	Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge
Q48886770	Visual exploration of structure-activity relationship using maximum common framework.
Q50141323	Visualisation and integration of G protein-coupled receptor related information help the modelling: description and applications of the Viseur program.
Q48057902	Visualisation and subsets of the chemical universe database GDB-13 for virtual screening
Q33913583	Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem
Q53596460	Visualization of multi-property landscapes for compound selection and optimization.
Q93119097	Visualizing protein-ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site
Q43887271	Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol
Q33226137	VolSurf analysis of pharmacokinetic properties for several antifungal sesquiterpene lactones isolated from Greek Centaurea sp.
Q62495668	WIZARD: AI in conformational analysis
Q40521899	WONKA: objective novel complex analysis for ensembles of protein-ligand structures.
Q29644511	Warfarin: history, tautomerism and activity
Q30642554	Warmr: a data mining tool for chemical data
Q68121901	Watching our numbers double
Q91524112	Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison
Q52300010	Wavelets and molecular structure.
Q91459321	Weak interactions in furan dimers
Q42059670	Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT.
Q45957087	Weighted voting-based consensus clustering for chemical structure databases.
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Q56973975	Why relevant chemical information cannot be exchanged without disclosing structures
Q83380497	Why you should read Dr. Cramer's perspective
Q47684449	Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort
Q48280343	Yada: a novel tool for molecular docking calculations.
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Q45958946	eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands.
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P6981	ACNP journal ID	44334
		2112742
		2112971
		927934
P8375	Crossref journal ID	2911
		3244
P1250	Danish Bibliometric Research Indicator (BFI) SNO/CNO	1091
P1058	ERA Journal ID	15245
P236	ISSN	0920-654X
		0928-2866
		1573-4951
		1573-9023
P1055	NLM Unique ID	8710425
		9418303
P10283	OpenAlex ID	V64621741
P3181	OpenCitations bibliographic resource ID	28716
		245276
P8104	Paperity journal ID	255923
P1156	Scopus source ID	24619
		55157
P5983	Springer journal ID	10822
P4616	UniProt journal ID	4057

P1240	Danish Bibliometric Research Indicator level	1
P8875	indexed in bibliographic review	Scopus	Q371467
		Science Citation Index Expanded	Q104047209
P407	language of work or name	English	Q1860
P123	publisher	Springer Science+Business Media	Q176916
P1813	short name	JCAMD
P1476	title	Journal of Computer - Aided Molecular Design
		Journal of Computer-Aided Molecular Design

Journal of Computer - Aided Molecular Design

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