Docking and scoring in virtual screening for drug discovery: methods and applications (scientific article)

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Q26740107	Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future
Q46213251	Hybrid Receptor-Bound/MM-GBSA-Per-residue Energy-Based Pharmacophore Modelling: Enhanced Approach for Identification of Selective LTA4H Inhibitors as Potential Anti-inflammatory Drugs
Q47994753	Hydroxytyrosol regulates the autophagy of vascular adventitial fibroblasts through the SIRT1-mediated signaling pathway
Q35690045	IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface
Q47780253	Identification and characterization of ErbB4 kinase inhibitors for effective breast cancer therapy
Q34787546	Identification of Hck inhibitors as hits for the development of antileukemia and anti-HIV agents
Q48834531	Identification of New Lead Molecules Against UBE2NL Enzyme for Cancer Therapy.
Q28548260	Identification of Novel Aldose Reductase Inhibitors from Spices: A Molecular Docking and Simulation Study
Q91644050	Identification of Novel PI3Kδ Selective Inhibitors by SVM-Based Multistage Virtual Screening and Molecular Dynamics Simulations
Q49804173	Identification of Novel Protein Kinase Receptor Type 2 Inhibitors Using Pharmacophore and Structure-Based Virtual Screening.
Q90284778	Identification of Potent VEGF Inhibitors for the Clinical Treatment of Glioblastoma, A Virtual Screening Approach
Q48022320	Identification of druggable targets for Acinetobacter baumannii via subtractive genomics and plausible inhibitors for MurA and MurB.
Q38958908	Identification of green tea catechins as potent inhibitors of the polo-box domain of polo-like kinase 1.
Q48365472	Identification of natural inhibitors of Bcr-Abl for the treatment of chronic myeloid leukemia.
Q40058742	Identification of new potent inhibitors of dengue virus NS3 protease from traditional Chinese medicine database
Q47279853	Identification of new potential HIV-1 reverse transcriptase inhibitors by QSAR modeling and structure-based virtual screening
Q92606226	Identification of novel antifungal agents: antimicrobial evaluation, SAR, ADME-Tox and molecular docking studies of a series of imidazole derivatives
Q92889749	Identification of potential agents for thymoma by integrated analyses of differentially expressed tumour-associated genes and molecular docking experiments
Q48321338	Identification of potential aryl hydrocarbon receptor ligands by virtual screening of industrial chemicals.
Q55692117	Identification of potential inhibitor targeting enoyl-acyl carrier protein reductase (InhA) in Mycobacterium tuberculosis: a computational approach.
Q45353103	Identification of potential inhibitors of H5N1 influenza A virus neuraminidase by ligand-based virtual screening approach
Q28485264	Identification of small molecule inhibitors of PTPσ through an integrative virtual and biochemical approach
Q41015632	Identification of small-molecule binding pockets in the soluble monomeric form of the Aβ42 peptide
Q36182445	Immunoinformatics Approach in Designing Epitope-based Vaccine Against Meningitis-inducing Bacteria (Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae Type b).
Q56919414	Impact of X-Ray Structure on Predictivity of Scoring Functions: PPARγ Case Study
Q37412834	Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction.
Q34219097	Improved cytochrome P450 3A4 molecular models accurately predict the Phe215 requirement for raloxifene dehydrogenation selectivity
Q54963827	Improving Docking Performance Using Negative Image-Based Rescoring.
Q38698230	Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015.
Q89152321	Improving small molecule virtual screening strategies for the next generation of therapeutics
Q91973876	In Silico Docking of Alkylphosphocholine Analogs to Human Serum Albumin Predicts Partitioning and Pharmacokinetics
Q36094897	In Silico Predictions of Drug - Drug Interactions Caused by CYP1A2, 2C9 and 3A4 Inhibition - a Comparative Study of Virtual Screening Performance
Q92944483	In Silico Structural Modeling and Analysis of Elongation Factor-1 Alpha and Elongation Factor-like Protein
Q46361570	In Silico Study and Bioprospection of the Antibacterial and Antioxidant Effects of Flavone and Its Hydroxylated Derivatives
Q35970006	In silico Analysis for Predicting Fatty Acids of Black Cumin Oil as Inhibitors of P-Glycoprotein
Q92863081	In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs
Q51746245	In silico Prediction and Wet Lab Validation of Arisaema tortuosum (Wall.) Schott Extracts as Antioxidant and Anti-breast Cancer Source: A Comparative Study.
Q42270323	In silico approach for the discovery of new PPARγ modulators among plant-derived polyphenols
Q36256916	In silico approaches and chemical space of anti-P-type ATPase compounds for discovering new antituberculous drugs.
Q27974727	In silico characterization of an atypical MAPK phosphatase of Plasmodium falciparum as a suitable target for drug discovery
Q38968891	In silico frameworks for systematic pre-clinical screening of potential anti-leukemia therapeutics
Q35097744	In silico identification and evaluation of leads for the simultaneous inhibition of protease and helicase activities of HCV NS3/4A protease using complex based pharmacophore mapping and virtual screening
Q30661799	In silico mechanistic analysis of IRF3 inactivation and high-risk HPV E6 species-dependent drug response
Q36840592	In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling
Q34185134	In silico screening of quadruplex-binding ligands
Q38638421	In silico studies in drug research against neurodegenerative diseases
Q52665081	In silico studies targeting G-protein coupled receptors for drug research against Parkinson's disease.
Q30353814	In silico study on multidrug resistance conferred by I223R/H275Y double mutant neuraminidase.
Q38783193	In vitro Cytotoxic Activities and Molecular Mechanisms of Angelica shikokiana Extract and its Isolated Compounds
Q87637133	In vitro antiamoebic activity evaluation and docking studies of metronidazole-triazole hybrids
Q29863457	In-Silico screening of Pleconaril and its novel substituted derivatives with Neuraminidase of H1N1 Influenza strain
Q39200387	In-silico analyses of sesquiterpene-related compounds on selected Leishmania enzyme-based targets.
Q48044225	Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks
Q89450851	Influence of gauche effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies
Q36496151	Inhibiting Helicobacter pylori HtrA protease by addressing a computationally predicted allosteric ligand binding site
Q36242811	Inhibition of bacterial virulence: drug-like molecules targeting the Salmonella enterica PhoP response regulator
Q35996541	Inhibition of neuraminidase by Ganoderma triterpenoids and implications for neuraminidase inhibitor design
Q51483259	Insight into the structural features of pyrazolopyrimidine- and pyrazolopyridine-based B-Raf(V600E) kinase inhibitors by computational explorations.
Q52361300	Integrating Experimental and In Silico HTS in the Discovery of Inhibitors of Protein-Nucleic Acid Interactions.
Q51872322	Integrating structure- and ligand-based virtual screening: comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets.
Q34967191	Integrating virtual and biochemical screening for protein tyrosine phosphatase inhibitor discovery.
Q64898800	Interaction of Tamoxifen Analogs With the Pocket Site of Some Hormone Receptors. A Molecular Docking and Density Functional Theory Study.
Q42255523	Interactions of ketoamide inhibitors on HCV NS3/4A protease target: molecular docking studies
Q60950229	Inverse Molecular Docking as a Novel Approach to Study Anticarcinogenic and Anti-Neuroinflammatory Effects of Curcumin
Q36252541	Investigating metabolite-protein interactions: an overview of available techniques
Q90241352	Investigation of Phospholipase Cγ1 Interaction with SLP76 Using Molecular Modeling Methods for Identifying Novel Inhibitors
Q88518698	Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data?
Q28833848	Is It Reliable to Use Common Molecular Docking Methods for Comparing the Binding Affinities of Enantiomer Pairs for Their Protein Target?
Q42361137	Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks
Q38032412	Iterative operations on microdroplets and continuous monitoring of processes within them; determination of solubility diagrams of proteins.
Q90193662	Key Topics in Molecular Docking for Drug Design
Q42285677	Kinetic characterizations of diallyl sulfide analogs for their novel role as CYP2E1 enzyme inhibitors
Q37544381	Knowing when to give up: early-rejection stratagems in ligand docking
Q36938240	Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles
Q37701430	LIBSA--a method for the determination of ligand-binding preference to allosteric sites on receptor ensembles
Q35570159	LOCAL KERNEL CANONICAL CORRELATION ANALYSIS WITH APPLICATION TO VIRTUAL DRUG SCREENING.
Q112609311	Learning protein-ligand binding affinity with atomic environment vectors
Q37053828	Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise
Q47414331	Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2.
Q36290790	LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders
Q36579823	Ligand binding mode prediction by docking: mdm2/mdmx inhibitors as a case study
Q36496975	Ligand discovery and virtual screening using the program LIDAEUS.
Q40898209	Ligand docking and binding site analysis with PyMOL and Autodock/Vina
Q35801074	Ligand similarity guided receptor selection enhances docking accuracy and recall for non-nucleoside HIV reverse transcriptase inhibitors
Q38896131	Ligand-based virtual screening under partial shape constraints
Q38031893	Ligand-receptor interaction platforms and their applications for drug discovery.
Q51891908	Ligand-specific scoring functions: improved ranking of docking solutions.
Q40254260	Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure-Based Design of Inhibitors for Trypsin-Like Serine Proteases
Q24813590	MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm
Q33327574	MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
Q45946918	Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening.
Q36951921	Machine learning methods and docking for predicting human pregnane X receptor activation
Q90324304	Machine learning prediction of oncology drug targets based on protein and network properties
Q50902844	Medicinal Chemistry Profiling of Monocyclic 1,2-Azaborines.
Q38865504	Medicinal Chemistry Strategies to Disrupt the p53-MDM2/MDMX Interaction.
Q34560447	Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines.
Q62515266	Metal–ligand interactions in drug design
Q50042689	Methyldopa blocks MHC class II binding to disease-specific antigens in autoimmune diabetes.
Q64926449	Microwave-Assisted Synthesis of Imidazo[4,5-f][1,10]phenanthroline Derivatives as Apoptosis Inducers in Chemotherapy by Stabilizing Bcl-2 G-quadruplex DNA.
Q54209288	Microwave-assisted synthesis of arene ruthenium(II) complexes [(η⁶-RC₆H₅)Ru(m-MOPIP)Cl]Cl (R = -H and -CH₃) as groove binder to c-myc G4 DNA.
Q64098229	Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α
Q50955545	Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking.
Q33309679	Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives
Q33602883	Modification of S-Adenosyl-l-Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation
Q89870017	Molecular Docking: From Lock and Key to Combination Lock
Q93126855	Molecular Docking: Shifting Paradigms in Drug Discovery
Q57176854	Molecular Modeling of Drug-Transporter Interactions-An International Transporter Consortium Perspective
Q50932369	Molecular Quantum Similarity, Chemical Reactivity and Database Screening of 3D Pharmacophores of the Protein Kinases A, B and G from Mycobacterium tuberculosis.
Q40105271	Molecular docking analysis of known flavonoids as duel COX-2 inhibitors in the context of cancer.
Q35519541	Molecular docking and inhibition studies on the interactions of Bacopa monnieri's potent phytochemicals against pathogenic Staphylococcus aureus.
Q41562707	Molecular docking and multivariate analysis of xanthones as antimicrobial and antiviral agents
Q26800097	Molecular docking and structure-based drug design strategies
Q26743663	Molecular docking as a popular tool in drug design, an in silico travel
Q52678127	Molecular docking based screening of Noggin inhibitors.
Q42750281	Molecular docking of bacosides with tryptophan hydroxylase: a model to understand the bacosides mechanism
Q37285667	Molecular docking studies for the identification of novel melatoninergic inhibitors for acetylserotonin-O-methyltransferase using different docking routines
Q35150471	Molecular docking: a powerful approach for structure-based drug discovery
Q53250654	Molecular dynamics simulation and density functional theory studies on the active pocket for the binding of paclitaxel to tubulin.
Q44409699	Molecular dynamics simulation study and molecular docking descriptors in structure-based QSAR on acetylcholinesterase (AChE) inhibitors
Q34061019	Molecular dynamics simulations and drug discovery
Q39494960	Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain.
Q47400742	Molecular dynamics simulations and novel drug discovery
Q28542431	Molecular investigations of protriptyline as a multi-target directed ligand in Alzheimer's disease
Q47298705	Molecular modeling and docking studies of the oxytocin receptor
Q58862097	Molecular modeling of plant metabolites with anti-Onchocerca activity
Q88046085	Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms
Q37843834	Molecular motions in drug design: the coming age of the metadynamics method
Q61455372	Molecules that Inhibit Bacterial Resistance Enzymes
Q101212027	MultiCon: A Semi-Supervised Approach for Predicting Drug Function from Chemical Structure Analysis
Q35096124	Multipose binding in molecular docking.
Q36457138	Mutation adjacent to the active site tyrosine can enhance DNA cleavage and cell killing by the TOPRIM Gly to Ser mutant of bacterial topoisomerase I.
Q38643859	Naphtho[1,2-b]furan-4,5-dione is a potent anti-MRSA agent against planktonic, biofilm and intracellular bacteria
Q59925168	Network of time-multiplexed optical parametric oscillators as a coherent Ising machine
Q36654909	New approaches to molecular cancer therapeutics
Q36390061	New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences.
Q34027266	New inhibitors of VEGFR-2 targeting the extracellular domain dimerization process
Q42326815	Nilotinib based pharmacophore models for BCRABL.
Q30248992	Norovirus drug candidates that inhibit viral capsid attachment to human histo-blood group antigens
Q99405141	Novel Bi-heterocycles as Potent Inhibitors of Urease and Less Cytotoxic Agents: 3-({5-((2-Amino-1,3-thiazol-4-yl)methyl)-1,3,4-oxadiazol-2-yl}sulfanyl)-N-(un/substituted-phenyl)propanamides
Q33703084	Novel Linear Peptides with High Affinity to αvβ3 Integrin for Precise Tumor Identification
Q35765639	Novel Scaffold Identification of mGlu1 Receptor Negative Allosteric Modulators Using a Hierarchical Virtual Screening Approach.
Q37543319	Novel codon insert in HIV type 1 clade B reverse transcriptase associated with low-level viremia during antiretroviral therapy.
Q90655635	Novel glitazones as PPARγ agonists: molecular design, synthesis, glucose uptake activity and 3D QSAR studies
Q34020313	Novel human mPGES-1 inhibitors identified through structure-based virtual screening
Q36939959	Novel inhibitors of checkpoint kinase 1.
Q47293289	Novel missense mutations in gidB gene associated with streptomycin resistance in Mycobacterium tuberculosis: insights from molecular dynamics
Q33567085	Novel mycosin protease MycP₁ inhibitors identified by virtual screening and 4D fingerprints
Q48197038	Novel pyridine-2,4,6-tricarbohydrazide thiourea compounds as small key organic molecules for the potential treatment of type-2 diabetes mellitus: In vitro studies against yeast α- and β-glucosidase and in silico molecular modeling.
Q47965977	Novel series of 1,2,4-trioxane derivatives as antimalarial agents
Q39033823	Octopus: a platform for the virtual high-throughput screening of a pool of compounds against a set of molecular targets
Q34481378	On scaffold hopping: challenges in the discovery of sulfated small molecules as mimetics of glycosaminoglycans
Q38674008	On the Integration of In Silico Drug Design Methods for Drug Repurposing
Q42106721	On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
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
Q34637014	Optimization and visualization of the edge weights in optimal assignment methods for virtual screening
Q28264356	Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
Q34625066	Optimization of molecular docking scores with support vector rank regression
Q50892827	Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect.
Q38818618	Overview of the SAMPL5 host-guest challenge: Are we doing better?
Q33320236	PDTD: a web-accessible protein database for drug target identification
Q42182002	PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements
Q34358460	PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions
Q39026290	PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking
Q59328919	Paradigm Shift in Drug Re-purposing From Phenalenone to Phenaleno-Furanone to Combat Multi-Drug Resistant Serovar Typhi
Q28486252	Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors
Q28534533	Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways
Q38179927	Pharmacoinformatic approaches to understand complexation of dendrimeric nanoparticles with drugs
Q35248674	Pharmacoinformatics approach for investigation of alternative potential hepatitis C virus nonstructural protein 5B inhibitors.
Q26772046	Pharmacophore Models and Pharmacophore-Based Virtual Screening: Concepts and Applications Exemplified on Hydroxysteroid Dehydrogenases
Q35395528	Pharmacophore modeling improves virtual screening for novel peroxisome proliferator-activated receptor-gamma ligands
Q38216045	Pharmacophore modeling technique applied for the discovery of proteasome inhibitors
Q34621241	Pharmacophore modelling: applications in drug discovery
Q42290292	Pharmacophore-Based Virtual Screening of Novel Inhibitors and Docking Analysis for CYP51A from Penicillium italicum
Q28530398	Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms
Q35870622	Plantamajoside, a potential anti-tumor herbal medicine inhibits breast cancer growth and pulmonary metastasis by decreasing the activity of matrix metalloproteinase-9 and -2.
Q37626063	Plasmodium falciparum: new molecular targets with potential for antimalarial drug development
Q30377334	PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity.
Q47355897	Potential natural mTOR inhibitors screened by in silico approach and suppress hepatic stellate cells activation.
Q92416641	Predicting kinase inhibitors using bioactivity matrix derived informer sets
Q90248056	Predicting or Pretending: Artificial Intelligence for Protein-Ligand Interactions Lack of Sufficiently Large and Unbiased Datasets
Q33900947	Predicting perfect drug candidates: Molecular docking 2.0.
Q35092840	Predicting target-ligand interactions using protein ligand-binding site and ligand substructures
Q34669773	Predicting the accuracy of protein-ligand docking on homology models.
Q53185669	Predicting the relative binding affinity of mineralocorticoid receptor antagonists by density functional methods.
Q37563518	Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme
Q40809353	Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism
Q35073109	Predictive power of molecular dynamics receptor structures in virtual screening
Q28485175	Probabilistic prediction of contacts in protein-ligand complexes
Q34516171	Probing molecular docking in a charged model binding site
Q21133564	Prospecting for novel plant-derived molecules of Rauvolfia serpentina as inhibitors of Aldose Reductase, a potent drug target for diabetes and its complications
Q35615893	Prospective performance evaluation of selected common virtual screening tools. Case study: Cyclooxygenase (COX) 1 and 2.
Q39719414	Protease Inhibitors in View of Peptide Substrate Databases
Q57990955	Protein Ligand DockingDocking in Drug DiscoveryDrug Discovery
Q90589166	Protein Preparation Automatic Protocol for High-Throughput Inverse Virtual Screening: Accelerating the Target Identification by Computational Methods
Q44012277	Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
Q47706285	Protein tyrosine phosphatase 1B inhibitory activity of cone oils from Juniperus chinensis cv. Kaizuca and in silico theoretical explanation
Q45716121	Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions.
Q107482904	Proteo-chemometrics interaction fingerprints of protein–ligand complexes predict binding affinity
Q28481635	Proteochemometric modeling of the bioactivity spectra of HIV-1 protease inhibitors by introducing protein-ligand interaction fingerprint
Q33790112	Pterostilbene, a Methoxylated Resveratrol Derivative, Efficiently Eradicates Planktonic, Biofilm, and Intracellular MRSA by Topical Application
Q36343105	PyGOLD: A python based API for docking based virtual screening workflow generation.
Q30381629	Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.
Q39677901	QSAR Models at the US FDA/NCTR.
Q57019425	QSAR and Molecular Modeling Approaches for Prediction of Drug Metabolism
Q38584487	Quantitative structure-activity relationship: promising advances in drug discovery platforms
Q55016340	Quantum Chemical Approaches in Structure-Based Virtual Screening and Lead Optimization.
Q41633463	Quantum mechanics implementation in drug-design workflows: does it really help?
Q44262192	Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge
Q38028555	Rational design of CCR2 antagonists: a survey of computational studies
Q34460848	ReFlexIn: a flexible receptor protein-ligand docking scheme evaluated on HIV-1 protease
Q39152860	Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors
Q57175255	Recent Trends and Applications of Molecular Modeling in GPCR⁻Ligand Recognition and Structure-Based Drug Design
Q33443633	Recent advances in computer-aided drug design
Q34645067	Recent advances in proteasome inhibitor discovery
Q42958774	Receptor-based virtual screening of EGFR kinase inhibitors from the NCI diversity database.
Q99614761	Recognition of Potential COVID-19 Drug Treatments through the Study of Existing Protein-Drug and Protein-Protein Structures: An Analysis of Kinetically Active Residues
Q40475389	Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv.
Q92243083	Refinement and Rescoring of Virtual Screening Results
Q39067502	Refinement, Reduction, and Replacement of Animal Toxicity Tests by Computational Methods
Q36764009	Regulation of protein-ligand binding affinity by hydrogen bond pairing.
Q30357425	Related genes and potential biomarkers for early diagnosis of Alzheimer's disease: a preliminary study based on DNA microarray.
Q37159748	Repositioning organohalogen drugs: a case study for identification of potent B-Raf V600E inhibitors via docking and bioassay
Q31027566	Representativity of target families in the Protein Data Bank: impact for family-directed structure-based drug discovery
Q90998969	Retrofitting metal-organic frameworks
Q48059059	Revealing the importance of linkers in K-series oxime reactivators for tabun-inhibited AChE using quantum chemical, docking and SMD studies.
Q38191684	Reverse docking: a powerful tool for drug repositioning and drug rescue
Q38088324	Review of knowledge for rational design and identification of anti-tubercular compounds
Q39004198	Rigid-Docking Approaches to Explore Protein-Protein Interaction Space.
Q43891873	Role of interactions and volume variation in discriminating active and inactive forms of cyclin-dependent kinase-2 inhibitor complexes
Q99246229	SARS-CoV Mpro inhibitory activity of aromatic disulfide compounds: QSAR model
Q33878164	SPA-LN: a scoring function of ligand-nucleic acid interactions via optimizing both specificity and affinity
Q34530633	Sanjeevini: a freely accessible web-server for target directed lead molecule discovery
Q58794823	Scaffolds as Structural Tools for Bone-Targeted Drug Delivery
Q36969891	Schnurri-3 is an essential regulator of osteoblast function and adult bone mass
Q36944104	Screening Outside the Catalytic Site: Inhibition of Macromolecular Inter-actions Through Structure-Based Virtual Ligand Screening Experiments.
Q38297767	Screening alpha-glucosidase and alpha-amylase inhibitors from natural compounds by molecular docking in silico
Q35878687	Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening
Q54541635	Selective flexibility of side-chain residues improves VEGFR-2 docking score using AutoDock Vina.
Q33957695	SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties
Q33374550	Side-chain conformational space analysis (SCSA): a multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities
Q96834102	Signature-based approaches for informed drug repurposing: targeting CNS disorders
Q48538413	Similarity search combined with docking and molecular dynamics for novel hAChE inhibitor scaffolds.
Q46888109	Similarity study of serine proteases inhibitors
Q28728561	Software and resources for computational medicinal chemistry
Q35819956	Specificity quantification of biomolecular recognition and its implication for drug discovery
Q92097004	Stalis: A Computational Method for Template-Based Ab Initio Ligand Design
Q94602027	State-of-the-art tools unveil potent drug targets amongst clinically approved drugs to inhibit helicase in SARS-CoV-2
Q35794917	Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition
Q89750991	Strategies for targeting the cardiac sarcomere: avenues for novel drug discovery
Q51539813	Structural Basis and Mechanism of Chiral Benzedrine Molecules Interacting With Third Dopamine Receptor.
Q26768150	Structural Features of Ion Transport and Allosteric Regulation in Sodium-Calcium Exchanger (NCX) Proteins
Q41343506	Structural basis for PPAR partial or full activation revealed by a novel ligand binding mode
Q36416631	Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery
Q28259532	Structural biology and drug discovery
Q35586235	Structural dynamics and inhibitor searching for Wnt-4 protein using comparative computational studies
Q48542611	Structural ensemble-based docking simulation and biophysical studies discovered new inhibitors of Hsp90 N-terminal domain.
Q92876781	Structural insights into NS5B protein of novel equine hepaciviruses and pegiviruses complexed with polymerase inhibitors
Q47412161	Structural insights into the binding mode of flavonols with the active site of matrix metalloproteinase-9 through molecular docking and molecular dynamic simulations studies
Q30587389	Structural protein-ligand interaction fingerprints (SPLIF) for structure-based virtual screening: method and benchmark study
Q35669512	Structural requirements of N-substituted spiropiperidine analogues as agonists of nociceptin/orphanin FQ receptor
Q92860595	Structural, functional, and stability change predictions in human telomerase upon specific point mutations
Q56854167	Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies
Q57697072	Structure-Based Discovery and Experimental Verification of Novel AI-2 Quorum Sensing Inhibitors againstVibrio harveyi
Q39750808	Structure-Based Pharmacophores for Virtual Screening
Q36055836	Structure-Based Virtual Screening of Commercially Available Compound Libraries
Q36546173	Structure-activity relationships and molecular modeling of 1,2,4-triazoles as adenosine receptor antagonists
Q46522604	Structure-based design of Aurora A & B inhibitors.
Q36394817	Structure-based design of novel combinatorially generated NBTIs as potential DNA gyrase inhibitors against various Staphylococcus aureus mutant strains.
Q42121557	Structure-based predictions of activity cliffs
Q43865391	Structure-based screening of inhibitors against KPC-2: designing potential drug candidates against multidrug-resistant bacteria
Q34063488	Structure-based selection of small molecules to alter allele-specific MHC class II antigen presentation
Q33495403	Structure-based substrate screening for an enzyme
Q33657421	Studies of metabolite-protein interactions: a review
Q90138871	Study of novel triazolo-benzodiazepine analogues as antidepressants targeting by molecular docking and ADMET properties prediction
Q35898338	Study of the Binding Energies between Unnatural Amino Acids and Engineered Orthogonal Tyrosyl-tRNA Synthetases
Q50212993	Study on Wangzaozin-A-Inducing Cancer Apoptosis and Its Theoretical Protein Targets.
Q89983464	Substrate Specific Inhibitor Designed against the Immunomodulator GMF-beta Reversed the Experimental Autoimmune Encephalomyelitis
Q26823990	Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors
Q47316545	Symmetrical Parameterization of Rigid Body Transformations for Biomolecular Structures
Q91845596	Synergistic Effect of Chlorogenic Acid and Caffeic Acid with Fosfomycin on Growth Inhibition of a Resistant Listeria monocytogenes Strain
Q92335202	Synthesis and Evaluation of Anisomelic acid-like Compounds for the Treatment of HPV-Mediated Carcinomas
Q34423599	Synthesis and in silico screening of a library of β-carboline-containing compounds
Q91933239	Synthesis and preclinical validation of novel P2Y1 receptor ligands as a potent anti-prostate cancer agent
Q99635133	Synthesis, In Silico and In Vitro Evaluation for Acetylcholinesterase and BACE-1 Inhibitory Activity of Some N-Substituted-4-Phenothiazine-Chalcones
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review article	Q7318358
scholarly article	Q13442814

P356	DOI	10.1038/NRD1549
P2888	exact match	https://scigraph.springernature.com/pub.10.1038/nrd1549
P698	PubMed publication ID	15520816
P5875	ResearchGate publication ID	8199343

P50	author	Jürgen Bajorath	Q18609784
P2093	author name string	Douglas B Kitchen
		Hélène Decornez
		John R Furr
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P433	issue	11
P921	main subject	drug discovery	Q1418791
		virtual screening	Q4112105
		drug screening	Q10505555
P304	page(s)	935-949
P577	publication date	2004-11-01
P1433	published in	Nature Reviews Drug Discovery	Q45998
P1476	title	Docking and scoring in virtual screening for drug discovery: methods and applications
P478	volume	3

Docking and scoring in virtual screening for drug discovery: methods and applications

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