Published in J Med Chem on October 05, 2006
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem (2009) 23.19
Efficient drug lead discovery and optimization. Acc Chem Res (2009) 2.90
The Enzyme Function Initiative. Biochemistry (2011) 1.87
In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. Br J Pharmacol (2007) 1.77
Target flexibility: an emerging consideration in drug discovery and design. J Med Chem (2008) 1.74
Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol (2008) 1.57
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. Bioinformatics (2010) 1.48
Minimal pharmacophoric elements and fragment hopping, an approach directed at molecular diversity and isozyme selectivity. Design of selective neuronal nitric oxide synthase inhibitors. J Am Chem Soc (2008) 1.47
Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol (2009) 1.47
Assessment of ligand-binding residue predictions in CASP9. Proteins (2011) 1.47
CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions. J Chem Inf Model (2011) 1.42
Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action. Genome Biol (2010) 1.42
Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein Sci (2009) 1.35
Discovery and characterization of a small molecule inhibitor of the PDZ domain of dishevelled. J Biol Chem (2009) 1.34
Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets. J Chem Inf Model (2007) 1.29
Predicting new indications for approved drugs using a proteochemometric method. J Med Chem (2012) 1.29
Computer-aided drug discovery and development (CADDD): in silico-chemico-biological approach. Chem Biol Interact (2006) 1.26
Rapid flexible docking using a stochastic rotamer library of ligands. J Chem Inf Model (2010) 1.21
Limits of Free Energy Computation for Protein-Ligand Interactions. J Chem Theory Comput (2010) 1.18
Funnel metadynamics as accurate binding free-energy method. Proc Natl Acad Sci U S A (2013) 1.17
CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series. J Chem Inf Model (2013) 1.17
From docking false-positive to active anti-HIV agent. J Med Chem (2007) 1.16
Assessment of ligand binding residue predictions in CASP8. Proteins (2009) 1.14
MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. BMC Bioinformatics (2008) 1.07
Docking screens: right for the right reasons? Curr Top Med Chem (2009) 1.05
Discovery of novel potent ΔF508-CFTR correctors that target the nucleotide binding domain. EMBO Mol Med (2013) 1.04
Improved ligand-protein binding affinity predictions using multiple binding modes. Biophys J (2010) 1.04
Sampling protein motion and solvent effect during ligand binding. Proc Natl Acad Sci U S A (2012) 1.04
Evaluation of machine-learning methods for ligand-based virtual screening. J Comput Aided Mol Des (2007) 1.03
CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. J Chem Inf Model (2013) 1.02
In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking. Proteins (2008) 1.01
Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface (2012) 1.01
Further analysis and comparative study of intermolecular interactions using dimers from the S22 database. J Chem Phys (2009) 1.01
Improving database enrichment through ensemble docking. J Comput Aided Mol Des (2008) 1.00
A kernel for open source drug discovery in tropical diseases. PLoS Negl Trop Dis (2009) 1.00
Discovery of novel fibroblast growth factor receptor 1 kinase inhibitors by structure-based virtual screening. J Med Chem (2010) 0.99
Machine learning methods and docking for predicting human pregnane X receptor activation. Chem Res Toxicol (2008) 0.99
Discovery of novel small-molecule inhibitors of BRD4 using structure-based virtual screening. J Med Chem (2013) 0.99
Pairwise additivity of energy components in protein-ligand binding: the HIV II protease-Indinavir case. J Chem Phys (2011) 0.97
Design of protein membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V. Proc Natl Acad Sci U S A (2007) 0.96
Protein flexibility in docking and surface mapping. Q Rev Biophys (2012) 0.96
Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction. J Am Chem Soc (2009) 0.96
Small-molecule ligand docking into comparative models with Rosetta. Nat Protoc (2013) 0.96
Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model (2011) 0.95
Enhanced ranking of PknB Inhibitors using data fusion methods. J Cheminform (2013) 0.95
Identification of alternative binding sites for inhibitors of HIV-1 ribonuclease H through comparative analysis of virtual enrichment studies. J Chem Inf Model (2011) 0.93
Can we use docking and scoring for hit-to-lead optimization? J Comput Aided Mol Des (2008) 0.93
Molecular dynamics simulations of GABA binding to the GABAC receptor: the role of Arg104. Biophys J (2008) 0.92
Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity? J Chem Inf Model (2014) 0.92
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. J Comput Aided Mol Des (2011) 0.90
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. J Comput Aided Mol Des (2014) 0.89
Assessing hERG pore models as templates for drug docking using published experimental constraints: the inactivated state in the context of drug block. J Chem Inf Model (2014) 0.88
Calculations of protein-ligand binding entropy of relative and overall molecular motions. J Comput Aided Mol Des (2007) 0.88
Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK. J Comput Aided Mol Des (2012) 0.88
Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding. PLoS One (2013) 0.87
Screening Outside the Catalytic Site: Inhibition of Macromolecular Inter-actions Through Structure-Based Virtual Ligand Screening Experiments. Open Biochem J (2008) 0.86
Structure-activity relationships and mechanism of action of Eph-ephrin antagonists: interaction of cholanic acid with the EphA2 receptor. ChemMedChem (2012) 0.86
Bringing Clarity to the Prediction of Protein-Ligand Binding Free Energies via "Blurring" J Chem Theory Comput (2014) 0.86
An interaction-motif-based scoring function for protein-ligand docking. BMC Bioinformatics (2010) 0.85
SHEF: a vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces. J Mol Model (2008) 0.84
Binding affinity prediction with property-encoded shape distribution signatures. J Chem Inf Model (2010) 0.84
Novel mycosin protease MycP₁ inhibitors identified by virtual screening and 4D fingerprints. J Chem Inf Model (2014) 0.83
Automated site preparation in physics-based rescoring of receptor ligand complexes. Proteins (2009) 0.83
VSDMIP: virtual screening data management on an integrated platform. J Comput Aided Mol Des (2008) 0.83
Calculating the sensitivity and robustness of binding free energy calculations to force field parameters. J Chem Theory Comput (2013) 0.83
Improved estimation of ligand-macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods. J Comput Aided Mol Des (2007) 0.83
Discovery of novel checkpoint kinase 1 inhibitors by virtual screening based on multiple crystal structures. J Chem Inf Model (2011) 0.83
Scoring confidence index: statistical evaluation of ligand binding mode predictions. J Comput Aided Mol Des (2009) 0.83
Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening. Curr Med Chem (2008) 0.83
Molecular motions in drug design: the coming age of the metadynamics method. J Comput Aided Mol Des (2011) 0.83
Knowledge-based fragment binding prediction. PLoS Comput Biol (2014) 0.83
The role of molecular simulations in the development of inhibitors of amyloid β-peptide aggregation for the treatment of Alzheimer's disease. ACS Chem Neurosci (2012) 0.82
One Size Does Not Fit All: The Limits of Structure-Based Models in Drug Discovery. J Chem Theory Comput (2013) 0.82
Using free energy of binding calculations to improve the accuracy of virtual screening predictions. J Chem Inf Model (2011) 0.82
A fragment-based approach to the SAMPL3 Challenge. J Comput Aided Mol Des (2012) 0.82
Application of docking-based comparative intermolecular contacts analysis to validate Hsp90α docking studies and subsequent in silico screening for inhibitors. J Mol Model (2012) 0.81
Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening. Wiley Interdiscip Rev Comput Mol Sci (2015) 0.81
Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model. J Chem Inf Model (2009) 0.81
IspE inhibitors identified by a combination of in silico and in vitro high-throughput screening. PLoS One (2012) 0.81
Evaluation of a Bayesian inference network for ligand-based virtual screening. J Cheminform (2009) 0.81
Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. J Comput Aided Mol Des (2012) 0.81
Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms. BMC Bioinformatics (2007) 0.80
Determination of locked interfaces in biomolecular complexes using Haptimol_RD. Biophys Physicobiol (2016) 0.80
Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods. Int J Mol Sci (2016) 0.80
Exploring the ligand-protein networks in traditional chinese medicine: current databases, methods, and applications. Evid Based Complement Alternat Med (2013) 0.80
A Novel Scoring Based Distributed Protein Docking Application to Improve Enrichment. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.80
Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin. J Comput Aided Mol Des (2009) 0.79
Proteochemometric modeling of the bioactivity spectra of HIV-1 protease inhibitors by introducing protein-ligand interaction fingerprint. PLoS One (2012) 0.79
FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols. J Mol Model (2012) 0.79
Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration. Biophys J (2011) 0.79
E/Z Energetics for Molecular Modeling and Design. J Chem Theory Comput (2010) 0.79
Energy Minimization on Manifolds for Docking Flexible Molecules. J Chem Theory Comput (2015) 0.79
The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators. J Comput Aided Mol Des (2014) 0.78
Small molecule inhibitors of hantavirus infection. Bioorg Med Chem Lett (2010) 0.78
Path-integral method for predicting relative binding affinities of protein-ligand complexes. J Am Chem Soc (2009) 0.78
Computer-based design of novel HIV-1 entry inhibitors: neomycin conjugated to arginine peptides at two specific sites. J Mol Model (2008) 0.78
Ligand- and receptor-based docking with LiBELa. J Comput Aided Mol Des (2015) 0.77
Porphyrin derivatives as inhibitors for acetylcholinesterase from Drosophila melanogaster. Bioinformation (2013) 0.77
Binding interactions of porphyrin derivatives with Ca(2+) ATPase of sarcoplasmic reticulum (SERCA1a). Bioinformation (2013) 0.77
New molecular scaffolds for the design of Mycobacterium tuberculosis type II dehydroquinase inhibitors identified using ligand and receptor based virtual screening. J Mol Model (2009) 0.76
ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model (2005) 16.75
Predicting new molecular targets for known drugs. Nature (2009) 9.71
Thousands of chemical starting points for antimalarial lead identification. Nature (2010) 8.28
Relating protein pharmacology by ligand chemistry. Nat Biotechnol (2007) 6.61
A critical assessment of docking programs and scoring functions. J Med Chem (2006) 5.78
A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J Med Chem (2002) 5.67
Benchmarking sets for molecular docking. J Med Chem (2006) 5.57
High-throughput assays for promiscuous inhibitors. Nat Chem Biol (2005) 4.32
A specific mechanism of nonspecific inhibition. J Med Chem (2003) 3.93
Large-scale prediction and testing of drug activity on side-effect targets. Nature (2012) 3.88
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol (2002) 3.71
Structure-based activity prediction for an enzyme of unknown function. Nature (2007) 3.65
Identification and prediction of promiscuous aggregating inhibitors among known drugs. J Med Chem (2003) 3.44
Small-molecule aggregates inhibit amyloid polymerization. Nat Chem Biol (2008) 2.98
A high-throughput screen for aggregation-based inhibition in a large compound library. J Med Chem (2007) 2.97
A model binding site for testing scoring functions in molecular docking. J Mol Biol (2002) 2.94
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem (2012) 2.86
A detergent-based assay for the detection of promiscuous inhibitors. Nat Protoc (2006) 2.58
Structure-based discovery of beta2-adrenergic receptor ligands. Proc Natl Acad Sci U S A (2009) 2.48
Predicting absolute ligand binding free energies to a simple model site. J Mol Biol (2007) 2.19
Deconstructing fragment-based inhibitor discovery. Nat Chem Biol (2006) 2.19
Automated docking screens: a feasibility study. J Med Chem (2009) 2.14
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem (2002) 2.10
Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol (2011) 2.10
Quantifying the relationships among drug classes. J Chem Inf Model (2008) 1.92
Structural bases of stability-function tradeoffs in enzymes. J Mol Biol (2002) 1.91
Kinase inhibitors: not just for kinases anymore. J Med Chem (2003) 1.90
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol (2009) 1.90
The Enzyme Function Initiative. Biochemistry (2011) 1.87
Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc (2006) 1.81
An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation. J Am Chem Soc (2002) 1.81
Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. J Med Chem (2008) 1.81
Hierarchical docking of databases of multiple ligand conformations. Curr Top Med Chem (2005) 1.79
Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors. J Am Chem Soc (2008) 1.74
Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol (2004) 1.73
Structure-based discovery of A2A adenosine receptor ligands. J Med Chem (2010) 1.71
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem (2003) 1.70
Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase. Structure (2002) 1.70
Promiscuous aggregate-based inhibitors promote enzyme unfolding. J Med Chem (2009) 1.68
Rapid context-dependent ligand desolvation in molecular docking. J Chem Inf Model (2010) 1.66
Quantifying biogenic bias in screening libraries. Nat Chem Biol (2009) 1.66
A pharmacological organization of G protein-coupled receptors. Nat Methods (2013) 1.65
Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci (2002) 1.61
Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat Chem Biol (2009) 1.60
Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol (2008) 1.57
Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem (2010) 1.54
Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase. Structure (2002) 1.54
Soft docking and multiple receptor conformations in virtual screening. J Med Chem (2004) 1.47
Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol (2009) 1.47
Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. Biochemistry (2009) 1.47
In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding. PLoS Biol (2013) 1.47
Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry (2005) 1.46
Structure-based approach for binding site identification on AmpC beta-lactamase. J Med Chem (2002) 1.45
Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease. J Med Chem (2010) 1.45
Decoys for docking. J Med Chem (2005) 1.43
Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough. J Biol Chem (2003) 1.43
Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J Med Chem (2006) 1.42
Nanomolar inhibitors of AmpC beta-lactamase. J Am Chem Soc (2003) 1.41
Structural basis for imipenem inhibition of class C beta-lactamases. Antimicrob Agents Chemother (2002) 1.39
Stability and equilibria of promiscuous aggregates in high protein milieus. Mol Biosyst (2007) 1.38
Chemical informatics and target identification in a zebrafish phenotypic screen. Nat Chem Biol (2011) 1.37
Identifying mechanism-of-action targets for drugs and probes. Proc Natl Acad Sci U S A (2012) 1.36
Molecular docking screens using comparative models of proteins. J Chem Inf Model (2009) 1.36
Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase. Biochemistry (2005) 1.32
The chemical basis of pharmacology. Biochemistry (2010) 1.30
Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET. Proc Natl Acad Sci U S A (2011) 1.29
Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams. Proteins (2002) 1.27
Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4. Proc Natl Acad Sci U S A (2012) 1.25
Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases. J Mol Biol (2007) 1.22
Probing molecular docking in a charged model binding site. J Mol Biol (2006) 1.17
Colloidal aggregation affects the efficacy of anticancer drugs in cell culture. ACS Chem Biol (2012) 1.17
The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34. J Biol Chem (2002) 1.16
The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. J Am Chem Soc (2006) 1.16
Structure-based discovery of antagonists of nuclear receptor LRH-1. J Biol Chem (2013) 1.16
Structural bases for stability-function tradeoffs in antibiotic resistance. J Mol Biol (2009) 1.16
Allosteric inhibition through core disruption. J Mol Biol (2004) 1.14
Colloidal aggregation causes inhibition of G protein-coupled receptors. J Med Chem (2013) 1.13
Docking for fragment inhibitors of AmpC beta-lactamase. Proc Natl Acad Sci U S A (2009) 1.13
The presynaptic component of the serotonergic system is required for clozapine's efficacy. Neuropsychopharmacology (2010) 1.09
Resolution of chiral phosphate, phosphonate, and phosphinate esters by an enantioselective enzyme library. J Am Chem Soc (2006) 1.08
Exploiting ordered waters in molecular docking. J Med Chem (2008) 1.07
Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol (2013) 1.05
Crystal structures of penicillin-binding protein 6 from Escherichia coli. J Am Chem Soc (2009) 1.05
Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture. J Am Chem Soc (2005) 1.05
Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase. J Mol Biol (2008) 1.05
Colloid formation by drugs in simulated intestinal fluid. J Med Chem (2010) 1.04
The hunt for 8-oxoguanine deaminase. J Am Chem Soc (2010) 1.04
Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB. J Med Chem (2010) 1.04
Colloidal drug formulations can explain "bell-shaped" concentration-response curves. ACS Chem Biol (2014) 1.04
Recognition and resistance in TEM beta-lactamase. Biochemistry (2003) 1.03
Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. ACS Chem Biol (2013) 1.01
Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo. Proc Natl Acad Sci U S A (2012) 1.00
Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc (2011) 1.00
The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution. J Am Chem Soc (2007) 1.00
Ligand pose and orientational sampling in molecular docking. PLoS One (2013) 0.99
Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs. J Med Chem (2010) 0.96
Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors. Bioorg Med Chem (2007) 0.96
Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry (2007) 0.96
Divergent modes of enzyme inhibition in a homologous structure-activity series. J Med Chem (2009) 0.96
Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model (2011) 0.95