Published in J Med Chem on January 26, 2006
Crystal structure of a lipid G protein-coupled receptor. Science (2012) 3.78
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des (2013) 2.93
Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure (2009) 2.83
Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol (2008) 2.38
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol (2007) 2.13
Molecular determinants of selectivity and efficacy at the dopamine D3 receptor. J Med Chem (2012) 1.87
The Enzyme Function Initiative. Biochemistry (2011) 1.87
Target flexibility: an emerging consideration in drug discovery and design. J Med Chem (2008) 1.74
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei. Proc Natl Acad Sci U S A (2008) 1.73
Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. J Chem Theory Comput (2008) 1.72
Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding. J Cell Biol (2008) 1.61
Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem (2010) 1.54
Advances and challenges in protein-ligand docking. Int J Mol Sci (2010) 1.54
Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des (2011) 1.53
The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. J Chem Theory Comput (2010) 1.52
Unique binding behavior of the recently approved angiotensin II receptor blocker azilsartan compared with that of candesartan. Hypertens Res (2012) 1.51
Lifting the lid on GPCRs: the role of extracellular loops. Br J Pharmacol (2012) 1.50
Crystal Structure of the Human Cannabinoid Receptor CB1. Cell (2016) 1.50
Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations. J Comput Aided Mol Des (2010) 1.41
Evaluation of homology modeling of G-protein-coupled receptors in light of the A(2A) adenosine receptor crystallographic structure. J Med Chem (2009) 1.38
Binding and orientation of tricyclic antidepressants within the central substrate site of the human serotonin transporter. J Biol Chem (2009) 1.38
The NanA neuraminidase of Streptococcus pneumoniae is involved in biofilm formation. Infect Immun (2009) 1.36
Molecular docking screens using comparative models of proteins. J Chem Inf Model (2009) 1.36
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
Protein phosphorylation and prevention of cytochrome oxidase inhibition by ATP: coupled mechanisms of energy metabolism regulation. Cell Metab (2011) 1.29
Binding of a small molecule at a protein-protein interface regulates the chaperone activity of hsp70-hsp40. ACS Chem Biol (2010) 1.28
Docking validation resources: protein family and ligand flexibility experiments. J Chem Inf Model (2010) 1.25
Structure-guided design of A(3) adenosine receptor-selective nucleosides: combination of 2-arylethynyl and bicyclo[3.1.0]hexane substitutions. J Med Chem (2012) 1.23
Fluoxetine (Prozac) binding to serotonin transporter is modulated by chloride and conformational changes. J Neurosci (2009) 1.23
A nonazole CYP51 inhibitor cures Chagas' disease in a mouse model of acute infection. Antimicrob Agents Chemother (2010) 1.22
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. J Comput Aided Mol Des (2012) 1.21
Rapid flexible docking using a stochastic rotamer library of ligands. J Chem Inf Model (2010) 1.21
Development of a unique small molecule modulator of CXCR4. PLoS One (2012) 1.18
Small molecule correctors of F508del-CFTR discovered by structure-based virtual screening. J Comput Aided Mol Des (2010) 1.17
Rational approaches to improving selectivity in drug design. J Med Chem (2012) 1.16
Response of a simian immunodeficiency virus (SIVmac251) to raltegravir: a basis for a new treatment for simian AIDS and an animal model for studying lentiviral persistence during antiretroviral therapy. Retrovirology (2010) 1.13
On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities. Proc Natl Acad Sci U S A (2012) 1.12
Discovery and structure-activity relationship analysis of Staphylococcus aureus sortase A inhibitors. Bioorg Med Chem (2009) 1.12
R-modafinil (armodafinil): a unique dopamine uptake inhibitor and potential medication for psychostimulant abuse. Biol Psychiatry (2012) 1.12
Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J Comput Aided Mol Des (2009) 1.11
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J Chem Inf Model (2009) 1.11
The binding sites for benztropines and dopamine in the dopamine transporter overlap. Neuropharmacology (2010) 1.11
Catalytic mechanism and three-dimensional structure of adenine deaminase. Biochemistry (2011) 1.11
Ligand-dependent conformations and dynamics of the serotonin 5-HT(2A) receptor determine its activation and membrane-driven oligomerization properties. PLoS Comput Biol (2012) 1.10
Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter. J Biol Chem (2012) 1.09
Emerging methods for ensemble-based virtual screening. Curr Top Med Chem (2010) 1.08
Predicting binding to p-glycoprotein by flexible receptor docking. PLoS Comput Biol (2011) 1.07
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des (2008) 1.07
Structure-function relationships of estrogenic triphenylethylenes related to endoxifen and 4-hydroxytamoxifen. J Med Chem (2010) 1.05
Improved ligand-protein binding affinity predictions using multiple binding modes. Biophys J (2010) 1.04
Involvement of the second extracellular loop and transmembrane residues of CCR5 in inhibitor binding and HIV-1 fusion: insights into the mechanism of allosteric inhibition. J Mol Biol (2008) 1.04
A unified model of the GABA(A) receptor comprising agonist and benzodiazepine binding sites. PLoS One (2013) 1.02
Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test. J Comput Aided Mol Des (2012) 1.01
Discovery of potent and reversible monoacylglycerol lipase inhibitors. Chem Biol (2009) 1.01
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PLoS Comput Biol (2010) 1.01
Discovery of a novel and potent class of F. tularensis enoyl-reductase (FabI) inhibitors by molecular shape and electrostatic matching. J Med Chem (2011) 1.01
Improving database enrichment through ensemble docking. J Comput Aided Mol Des (2008) 1.00
Unbiased simulations reveal the inward-facing conformation of the human serotonin transporter and Na(+) ion release. PLoS Comput Biol (2011) 1.00
Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc (2011) 1.00
Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. J Chem Theory Comput (2012) 0.99
Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors. J Comput Aided Mol Des (2012) 0.99
In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking. Proteins (2009) 0.98
Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chem Biol Drug Des (2013) 0.97
Protein flexibility in docking and surface mapping. Q Rev Biophys (2012) 0.96
Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process. J Chem Theory Comput (2013) 0.96
Docking-based virtual screening for ligands of G protein-coupled receptors: not only crystal structures but also in silico models. J Mol Graph Model (2010) 0.96
Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model (2011) 0.95
Chemical-biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target. Beilstein J Org Chem (2013) 0.95
Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain. Biochem J (2012) 0.95
In silico analysis of the binding of agonists and blockers to the β2-adrenergic receptor. J Mol Graph Model (2011) 0.94
A new mechanism of allostery in a G protein-coupled receptor dimer. Nat Chem Biol (2014) 0.93
Thiazolidinedione-based PI3Kα inhibitors: an analysis of biochemical and virtual screening methods. ChemMedChem (2011) 0.93
Binding-site assessment by virtual fragment screening. PLoS One (2010) 0.93
Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of alpha1-antitrypsin: implications for disease and drug design. J Mol Biol (2009) 0.93
Molecular modeling to provide insight into the substrate binding and catalytic mechanism of human biliverdin-IXα reductase. J Phys Chem B (2012) 0.93
Comparative modeling of the human monoamine transporters: similarities in substrate binding. ACS Chem Neurosci (2012) 0.92
A single glycine in extracellular loop 1 is the critical determinant for pharmacological specificity of dopamine D2 and D3 receptors. Mol Pharmacol (2013) 0.92
Understanding the molecular basis of HBV drug resistance by molecular modeling. Antiviral Res (2008) 0.92
Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway. Biochemistry (2010) 0.92
QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism. J Chem Theory Comput (2009) 0.91
Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. Acta Crystallogr D Biol Crystallogr (2008) 0.91
The marine cyanobacterial metabolite gallinamide A is a potent and selective inhibitor of human cathepsin L. J Nat Prod (2013) 0.91
Synthesis, biological evaluation and molecular modeling studies of N6-benzyladenosine analogues as potential anti-toxoplasma agents. Biochem Pharmacol (2007) 0.91
Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. J Am Chem Soc (2013) 0.90
Identification of novel agonists of the integrin CD11b/CD18. Bioorg Med Chem Lett (2009) 0.90
Flexible backbone sampling methods to model and design protein alternative conformations. Methods Enzymol (2013) 0.89
Discovery of Staphylococcus aureus sortase A inhibitors using virtual screening and the relaxed complex scheme. Chem Biol Drug Des (2013) 0.89
Using a homology model of cytochrome P450 2D6 to predict substrate site of metabolism. J Comput Aided Mol Des (2010) 0.88
Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation. J Comput Aided Mol Des (2009) 0.88
Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics (2012) 0.88
The two Na+ sites in the human serotonin transporter play distinct roles in the ion coupling and electrogenicity of transport. J Biol Chem (2013) 0.88
Rational design of alpha-conotoxin analogues targeting alpha7 nicotinic acetylcholine receptors: improved antagonistic activity by incorporation of proline derivatives. J Biol Chem (2009) 0.87
Aminorex, a metabolite of the cocaine adulterant levamisole, exerts amphetamine like actions at monoamine transporters. Neurochem Int (2013) 0.87
Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents. ACS Chem Biol (2015) 0.87
Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations. PLoS One (2013) 0.87
Novel method for probing the specificity binding profile of ligands: applications to HIV protease. Chem Biol Drug Des (2008) 0.87
Computational and biochemical docking of the irreversible cocaine analog RTI 82 directly demonstrates ligand positioning in the dopamine transporter central substrate-binding site. J Biol Chem (2014) 0.87
Inhibition of gastric tumor growth by a novel Hsp90 inhibitor. Biochem Pharmacol (2013) 0.86
Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem (2004) 7.96
A hierarchical approach to all-atom protein loop prediction. Proteins (2004) 5.18
Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comput Chem (2005) 3.71
Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proc Natl Acad Sci U S A (2007) 3.33
Dysregulated pH: a perfect storm for cancer progression. Nat Rev Cancer (2011) 3.10
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des (2013) 2.93
Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc Natl Acad Sci U S A (2005) 2.88
Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. J Am Chem Soc (2008) 2.81
SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production. Cell Metab (2010) 2.77
On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol (2002) 2.73
Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. J Comput Chem (2002) 2.59
PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des (2006) 2.53
Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol (2007) 2.29
Toward better refinement of comparative models: predicting loops in inexact environments. Proteins (2008) 2.06
Assessment of protein structure refinement in CASP9. Proteins (2011) 2.06
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
A kinematic view of loop closure. J Comput Chem (2004) 2.03
Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure (2008) 1.91
Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. J Phys Chem B (2008) 1.90
Mechanistic studies on the hydroxylation of methane by methane monooxygenase. Chem Rev (2003) 1.89
The Enzyme Function Initiative. Biochemistry (2011) 1.87
On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds. Nat Chem Biol (2011) 1.82
Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers. J Am Chem Soc (2006) 1.79
Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. J Am Chem Soc (2015) 1.76
Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. J Chem Theory Comput (2008) 1.72
SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. Cell Metab (2013) 1.70
Long loop prediction using the protein local optimization program. Proteins (2006) 1.64
Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry (2005) 1.62
Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding. J Cell Biol (2008) 1.61
Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol (2008) 1.57
Assessment of the protein-structure refinement category in CASP8. Proteins (2009) 1.53
Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides. J Am Chem Soc (2006) 1.52
Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study. J Am Chem Soc (2007) 1.50
Intracellular pH sensors: design principles and functional significance. Physiology (Bethesda) (2007) 1.46
Electronic structure of tubular aromatic molecules derived from the metallic (5,5) armchair single wall carbon nanotube. J Am Chem Soc (2004) 1.46
Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature (2013) 1.46
Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles. J Chem Theory Comput (2009) 1.45
Computer-aided antibody design. Protein Eng Des Sel (2012) 1.44
Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. J Chem Inf Model (2006) 1.43
Divergent evolution in enolase superfamily: strategies for assigning functions. J Biol Chem (2011) 1.40
Use of an induced fit receptor structure in virtual screening. Chem Biol Drug Des (2006) 1.40
Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling. Proteins (2007) 1.39
Dioxygen activation in methane monooxygenase: a theoretical study. J Am Chem Soc (2004) 1.38
Novel human lipoxygenase inhibitors discovered using virtual screening with homology models. J Med Chem (2006) 1.36
Computational modeling of the catalytic reaction in triosephosphate isomerase. J Mol Biol (2004) 1.36
Conformational changes in protein loops and helices induced by post-translational phosphorylation. PLoS Comput Biol (2006) 1.36
Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). J Phys Chem B (2011) 1.35
High-energy water sites determine peptide binding affinity and specificity of PDZ domains. Protein Sci (2009) 1.35
Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys (2006) 1.34
Turning a protein kinase on or off from a single allosteric site via disulfide trapping. Proc Natl Acad Sci U S A (2011) 1.33
Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily. J Mol Biol (2006) 1.31
Strengths of hydrogen bonds involving phosphorylated amino acid side chains. J Am Chem Soc (2007) 1.31
Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors. Proc Natl Acad Sci U S A (2011) 1.30
Structural characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei bound to the antifungal drugs posaconazole and fluconazole. PLoS Negl Trop Dis (2010) 1.30
Peripheral heme substituents control the hydrogen-atom abstraction chemistry in cytochromes P450. Proc Natl Acad Sci U S A (2003) 1.30
Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation. Proteins (2008) 1.29
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
Surfaces affect ion pairing. J Phys Chem B (2005) 1.29
Hydroxylation of methane by non-heme diiron enzymes: molecular orbital analysis of C-H bond activation by reactive intermediate Q. J Am Chem Soc (2002) 1.25
The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins (2011) 1.25
Protein side-chain dynamics and residual conformational entropy. J Am Chem Soc (2009) 1.25
A nonazole CYP51 inhibitor cures Chagas' disease in a mouse model of acute infection. Antimicrob Agents Chemother (2010) 1.22
Mixed quantum mechanical/molecular mechanical (QM/MM) study of the deacylation reaction in a penicillin binding protein (PBP) versus in a class C beta-lactamase. J Am Chem Soc (2004) 1.22
Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature (2013) 1.22
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. J Comput Aided Mol Des (2012) 1.21
Conformation switching of clathrin light chain regulates clathrin lattice assembly. Dev Cell (2010) 1.21
A role for a specific cholesterol interaction in stabilizing the Apo configuration of the human A(2A) adenosine receptor. Structure (2009) 1.19
Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc Natl Acad Sci U S A (2012) 1.17
Computational studies of protein regulation by post-translational phosphorylation. Curr Opin Struct Biol (2009) 1.16
A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations. J Comput Chem (2003) 1.16
Toward deciphering the code to aminergic G protein-coupled receptor drug design. Chem Biol (2008) 1.16
Computational prediction of native protein ligand-binding and enzyme active site sequences. Proc Natl Acad Sci U S A (2005) 1.14
Cytochrome P450CAM enzymatic catalysis cycle: a quantum mechanics/molecular mechanics study. J Am Chem Soc (2004) 1.13
Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis . Biochemistry (2009) 1.12
Reversible surface oxidation and efficient luminescence quenching in semiconductor single-wall carbon nanotubes. J Am Chem Soc (2004) 1.12
What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. J Comput Chem (2006) 1.12
On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities. Proc Natl Acad Sci U S A (2012) 1.12
Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases. ChemMedChem (2011) 1.11
Serial replica exchange. J Phys Chem B (2007) 1.11
Substrate hydroxylation in methane monooxygenase: quantitative modeling via mixed quantum mechanics/molecular mechanics techniques. J Am Chem Soc (2005) 1.10
Reversible dioxygen binding to hemerythrin. J Am Chem Soc (2003) 1.09
Modeling conformational ensembles of slow functional motions in Pin1-WW. PLoS Comput Biol (2010) 1.09
Reactions of methane monooxygenase intermediate Q with derivatized methanes. J Am Chem Soc (2002) 1.08
Predicting binding to p-glycoprotein by flexible receptor docking. PLoS Comput Biol (2011) 1.07
Multisite phosphorylation disrupts arginine-glutamate salt bridge networks required for binding of cytoplasmic linker-associated protein 2 (CLASP2) to end-binding protein 1 (EB1). J Biol Chem (2012) 1.06
Theoretical study of cisplatin binding to purine bases: why does cisplatin prefer guanine over adenine? J Am Chem Soc (2003) 1.06
Localized orbital corrections for the calculation of ionization potentials and electron affinities in density functional theory. J Phys Chem B (2006) 1.06
Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proc Natl Acad Sci U S A (2013) 1.06
Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study. J Am Chem Soc (2006) 1.05
Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance(). Medchemcomm (2012) 1.05
New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies. Bioorg Med Chem (2006) 1.04
Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery. J Am Chem Soc (2006) 1.04