| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/jcamd/AmaroBM08 |
| P356 | DOI | 10.1007/S10822-007-9159-2 |
| P2888 | exact match | https://scigraph.springernature.com/pub.10.1007/s10822-007-9159-2 |
| P932 | PMC publication ID | 2516539 |
| P698 | PubMed publication ID | 18196463 |
| P5875 | ResearchGate publication ID | 5655974 |
| P50 | author | J. Andrew McCammon | Q6104601 |
| P2093 | author name string | Riccardo Baron | |
| Rommie E Amaro | |||
| P2860 | cites work | On the evolution of structure in aminoacyl-tRNA synthetases | Q24597654 |
| Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein | Q27637510 | ||
| Small molecule binding to an artificially created cavity at the active site of cytochrome c peroxidase | Q27731261 | ||
| A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity | Q27732870 | ||
| Introduction of novel substrate oxidation into cytochrome c peroxidase by cavity complementation: oxidation of 2-aminothiazole and covalent modification of the enzyme | Q27744161 | ||
| All-atom empirical potential for molecular modeling and dynamics studies of proteins | Q27860468 | ||
| VMD: visual molecular dynamics | Q27860554 | ||
| Scalable molecular dynamics with NAMD | Q27860718 | ||
| Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings | Q27861111 | ||
| Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors | Q28219491 | ||
| Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei | Q28471703 | ||
| A semiempirical free energy force field with charge-based desolvation | Q29614316 | ||
| Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels | Q29615743 | ||
| Developing a dynamic pharmacophore model for HIV-1 integrase. | Q30326870 | ||
| Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information. | Q30350196 | ||
| Novel procedure for modeling ligand/receptor induced fit effects. | Q30352584 | ||
| Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. | Q30357936 | ||
| Exploring experimental sources of multiple protein conformations in structure-based drug design. | Q30362194 | ||
| Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations | Q31034789 | ||
| Solvated docking: introducing water into the modelling of biomolecular complexes. | Q31053010 | ||
| Ligand binding affinities from MD simulations. | Q31080599 | ||
| Molecular recognition and docking algorithms | Q31130825 | ||
| Binding site characteristics in structure-based virtual screening: evaluation of current docking tools | Q31135121 | ||
| Computational approaches to molecular recognition. | Q47829750 | ||
| Why is it so difficult to simulate entropies, free energies, and their differences? | Q49297337 | ||
| Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking. | Q51930103 | ||
| Critical assessment of the automated AutoDock as a new docking tool for virtual screening. | Q51932994 | ||
| 23 Theoretical calculations of relative affinities of binding | Q52464273 | ||
| An improved nucleic acid parameter set for the GROMOS force field | Q56225273 | ||
| Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling | Q57976077 | ||
| Enhancing the Effectiveness of Virtual Screening by Fusing Nearest Neighbor Lists: A Comparison of Similarity Coefficients | Q61960983 | ||
| A new method for predicting binding affinity in computer-aided drug design | Q72408636 | ||
| Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations | Q74452346 | ||
| Energetics of codon-anticodon recognition on the small ribosomal subunit | Q79468922 | ||
| Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions | Q79890296 | ||
| Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case | Q80850175 | ||
| Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase | Q83158635 | ||
| Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic Ligands | Q86840750 | ||
| Hydrogen Bonding, Hydrophobic Interactions, and Failure of the Rigid Receptor Hypothesis | Q88521517 | ||
| 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 | Q94466096 | ||
| Virtual screening of human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase against the NCI diversity set by use of AutoDock to identify novel nonfolate inhibitors | Q31136678 | ||
| Binding affinity prediction with different force fields: examination of the linear interaction energy method | Q33202843 | ||
| Structure-based development of target-specific compound libraries | Q33238328 | ||
| How good is your screening library? | Q33247826 | ||
| Receptor-based computational screening of compound databases: the main docking-scoring engines | Q33262082 | ||
| Free energies of ligand binding for structurally diverse compounds | Q33784228 | ||
| Chemoinformatics - predicting the physicochemical properties of 'drug-like' molecules | Q33840254 | ||
| The statistical-thermodynamic basis for computation of binding affinities: a critical review | Q33915676 | ||
| Evolutionary profiles from the QR factorization of multiple sequence alignments | Q33932608 | ||
| The many roles of computation in drug discovery | Q34307063 | ||
| Docking and scoring in virtual screening for drug discovery: methods and applications | Q34364227 | ||
| The GROMOS software for biomolecular simulation: GROMOS05. | Q34457783 | ||
| Discovery of a novel binding trench in HIV integrase. | Q34546744 | ||
| Protein flexibility and drug design: how to hit a moving target. | Q34754636 | ||
| Protein flexibility and computer-aided drug design | Q34762700 | ||
| Guiding molecules towards drug-likeness. | Q34798904 | ||
| A review of protein-small molecule docking methods | Q34937524 | ||
| Theoretical calculation of relative binding affinity in host-guest systems | Q35589506 | ||
| Comparing protein-ligand docking programs is difficult. | Q36152993 | ||
| The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase | Q36279350 | ||
| Accounting for global protein deformability during protein-protein and protein-ligand docking | Q36281420 | ||
| Molecular dynamics: survey of methods for simulating the activity of proteins | Q36472758 | ||
| Biomolecular modeling: Goals, problems, perspectives | Q36500277 | ||
| Protein-ligand docking: current status and future challenges | Q36544700 | ||
| A decade of fragment-based drug design: strategic advances and lessons learned | Q36732253 | ||
| Activity based probes for proteases: applications to biomarker discovery, molecular imaging and drug screening. | Q36741418 | ||
| Free energy via molecular simulation: applications to chemical and biomolecular systems | Q38648060 | ||
| High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1. | Q38970102 | ||
| Rapid non-empirical approaches for estimating relative binding free energies | Q41147994 | ||
| Determinants of ligand binding to cAMP-dependent protein kinase. | Q41608927 | ||
| Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations | Q42629821 | ||
| Computational drug design accommodating receptor flexibility: the relaxed complex scheme | Q43992973 | ||
| Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach | Q44054097 | ||
| The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme | Q44310443 | ||
| Principles of carbopeptoid folding: a molecular dynamics simulation study | Q45213929 | ||
| Representing receptor flexibility in ligand docking through relevant normal modes. | Q46211444 | ||
| An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei | Q46859677 | ||
| Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character | Q47442749 | ||
| P433 | issue | 9 | |
| P304 | page(s) | 693-705 | |
| P577 | publication date | 2008-01-15 | |
| P1433 | published in | Journal of Computer - Aided Molecular Design | Q15766522 |
| P1476 | title | An improved relaxed complex scheme for receptor flexibility in computer-aided drug design | |
| P478 | volume | 22 |
| Q92955278 | A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation |
| Q46689329 | A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds. |
| Q35373481 | A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer-aided Drug Discovery |
| Q92107770 | A comprehensive review of computational techniques for the prediction of drug side effects |
| Q30372843 | A continuous peptide epitope reacting with pandemic influenza AH1N1 predicted by bioinformatic approaches. |
| Q33758191 | A dynamic model of HIV integrase inhibition and drug resistance |
| Q55432485 | A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model. |
| Q33404791 | A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach |
| Q34402706 | ALiBERO: evolving a team of complementary pocket conformations rather than a single leader |
| Q28474233 | AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening |
| Q37281443 | Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor |
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| Q36950248 | Andrographolide derivatives inhibit guanine nucleotide exchange and abrogate oncogenic Ras function |
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| Q28740837 | Approximating protein flexibility through dynamic pharmacophore models: application to fatty acid amide hydrolase (FAAH) |
| Q30392142 | Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties |
| Q58719254 | Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview |
| Q30518005 | Catalytic transitions in the human MDR1 P-glycoprotein drug binding sites |
| Q36729008 | Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase |
| Q92369297 | Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation |
| Q52715489 | Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease. |
| Q38612789 | Computational allosteric ligand binding site identification on Ras proteins. |
| Q37375373 | Computational evaluation of protein-small molecule binding. |
| Q28475699 | Computational fragment-based binding site identification by ligand competitive saturation |
| Q24628577 | Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53 |
| Q28473888 | Computational identification of uncharacterized cruzain binding sites |
| Q30398071 | Computational methods in drug discovery. |
| Q28242602 | Computer-aided drug discovery approach finds calcium sensitizer of cardiac troponin |
| Q34519388 | Computer-aided drug-discovery techniques that account for receptor flexibility |
| Q33954211 | Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness |
| Q41382543 | Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes |
| Q33605053 | Current progress in patient-specific modeling |
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| Q37344732 | Discovery of Staphylococcus aureus sortase A inhibitors using virtual screening and the relaxed complex scheme |
| Q36960711 | Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei |
| Q37722604 | Discovery of novel inhibitors of HIV-1 reverse transcriptase through virtual screening of experimental and theoretical ensembles |
| Q90665064 | Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria |
| Q34680415 | Docking validation resources: protein family and ligand flexibility experiments |
| Q28475676 | Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis |
| Q35688079 | Drug screening strategy for human membrane proteins: from NMR protein backbone structure to in silica- and NMR-screened hits |
| Q36082949 | Drug search for leishmaniasis: a virtual screening approach by grid computing. |
| Q47374327 | Dynamic Docking: A Paradigm Shift in Computational Drug Discovery |
| Q36119273 | Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study |
| Q30421174 | Dynamics of Plasmodium falciparum enoyl-ACP reductase and implications on drug discovery |
| Q26851157 | Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach |
| Q34173532 | Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations |
| Q36803981 | Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. |
| Q43115469 | Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation |
| Q35211087 | Efficient incorporation of protein flexibility and dynamics into molecular docking simulations |
| Q35994201 | Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2. |
| Q30358225 | Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. |
| Q34908421 | Emerging methods for ensemble-based virtual screening |
| Q34610866 | Emerging topics in structure-based virtual screening. |
| Q48052175 | Energetics and structural characterization of the "DFG-flip" conformational transition of B-RAF kinase: a SITS molecular dynamics study |
| Q88238882 | Ensemble Docking in Drug Discovery |
| Q30370020 | Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. |
| Q27001129 | Exploring the role of receptor flexibility in structure-based drug discovery |
| Q34173497 | FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection. |
| Q36899690 | Farnesyl diphosphate synthase inhibitors from in silico screening |
| Q48059653 | Fragment-based virtual screening approach and molecular dynamics simulation studies for identification of BACE1 inhibitor leads |
| Q47348724 | GPCRs: What Can We Learn from Molecular Dynamics Simulations? |
| Q34106218 | Guide to virtual screening: application to the Akt phosphatase PHLPP. |
| Q35214824 | Hierarchical virtual screening approaches in small molecule drug discovery |
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| Q41998223 | Hybrid Steered Molecular Dynamics-Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target |
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