Published in Curr Pharm Des on January 01, 2011
Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry (2011) 1.14
Catalytic transitions in the human MDR1 P-glycoprotein drug binding sites. Biochemistry (2012) 0.98
Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. J Comput Chem (2012) 0.96
Protein flexibility in virtual screening: the BACE-1 case study. J Chem Inf Model (2012) 0.90
Multiple Drug Transport Pathways through Human P-Glycoprotein. Biochemistry (2015) 0.78
In silico mechanistic profiling to probe small molecule binding to sulfotransferases. PLoS One (2013) 0.78
Structural basis of resistance to anti-cytochrome bc₁ complex inhibitors: implication for drug improvement. Curr Pharm Des (2014) 0.77
Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors. Mem Inst Oswaldo Cruz (2015) 0.75
Drug search for leishmaniasis: a virtual screening approach by grid computing. J Comput Aided Mol Des (2016) 0.75
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
GROMACS: fast, flexible, and free. J Comput Chem (2005) 27.22
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem (2010) 25.20
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem (2009) 23.19
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem (2004) 15.51
Molecular dynamics simulations of biomolecules. Nat Struct Biol (2002) 7.68
Empirical force fields for biological macromolecules: overview and issues. J Comput Chem (2004) 7.49
The many roles of computation in drug discovery. Science (2004) 5.66
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys (2004) 5.00
Accelerating molecular modeling applications with graphics processors. J Comput Chem (2007) 4.83
Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem (2006) 4.74
Watching a protein as it functions with 150-ps time-resolved x-ray crystallography. Science (2003) 4.12
Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol (2009) 3.81
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci (2002) 3.01
Efficient drug lead discovery and optimization. Acc Chem Res (2009) 2.90
Implications of protein flexibility for drug discovery. Nat Rev Drug Discov (2003) 2.83
Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol (2004) 2.65
Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc (2002) 2.58
Protein flexibility and drug design: how to hit a moving target. Curr Opin Chem Biol (2002) 2.41
Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol (2008) 2.38
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci (2004) 2.34
Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc (2005) 2.32
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
Discovery of a novel binding trench in HIV integrase. J Med Chem (2004) 2.09
Accommodating protein flexibility in computational drug design. Mol Pharmacol (2000) 1.84
Protein NMR spectroscopy in structural genomics. Nat Struct Biol (2000) 1.80
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers (2003) 1.80
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
Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol (2004) 1.73
Developing a dynamic pharmacophore model for HIV-1 integrase. J Med Chem (2000) 1.71
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem (2003) 1.70
Combining docking and molecular dynamic simulations in drug design. Med Res Rev (2006) 1.70
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des (2008) 1.69
Ligand docking to proteins with discrete side-chain flexibility. J Mol Biol (1994) 1.60
Exploring experimental sources of multiple protein conformations in structure-based drug design. J Am Chem Soc (2007) 1.52
Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. J Med Chem (2005) 1.50
Soft docking and multiple receptor conformations in virtual screening. J Med Chem (2004) 1.47
Taking aim at a moving target: designing drugs to inhibit drug-resistant HIV-1 reverse transcriptases. Curr Opin Struct Biol (2004) 1.44
Conformational flexibility models for the receptor in structure based drug design. Curr Pharm Des (2003) 1.39
Non-nucleoside reverse transcriptase inhibitors (NNRTIs): past, present, and future. Chem Biodivers (2004) 1.37
High-throughput crystallization and structure determination in drug discovery. Drug Discov Today (2002) 1.30
Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models. J Am Chem Soc (2007) 1.28
Virtual screening in lead discovery and optimization. Curr Opin Drug Discov Devel (2004) 1.26
Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach. Chem Biol Drug Des (2010) 1.24
From virtuality to reality - Virtual screening in lead discovery and lead optimization: a medicinal chemistry perspective. Curr Opin Drug Discov Devel (2008) 1.24
Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach. J Am Chem Soc (2002) 1.20
Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective. Curr Opin Struct Biol (2002) 1.18
Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model (2010) 1.17
Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case. J Am Chem Soc (2004) 1.15
Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness. J Med Chem (2010) 1.13
High performance computing in biology: multimillion atom simulations of nanoscale systems. J Struct Biol (2006) 1.13
The flexible pocketome engine for structural chemogenomics. Methods Mol Biol (2009) 1.11
Recent development and application of virtual screening in drug discovery: an overview. Curr Pharm Des (2004) 1.10
Efficient molecular docking of NMR structures: application to HIV-1 protease. Protein Sci (2006) 1.09
Fully flexible low-mode docking: application to induced fit in HIV integrase. J Am Chem Soc (2001) 1.06
The 'dynamics' in the thermodynamics of binding. Nat Struct Biol (1999) 1.06
Target flexibility in molecular recognition. Biochim Biophys Acta (2005) 1.01
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PLoS Comput Biol (2010) 1.01
Molecular docking of balanol to dynamics snapshots of protein kinase A. Proteins (2005) 1.01
A dynamic model of HIV integrase inhibition and drug resistance. J Mol Biol (2010) 0.99
Recent advances in structure-based rational drug design. Curr Opin Struct Biol (2000) 0.99
Docking, virtual high throughput screening and in silico fragment-based drug design. J Cell Mol Med (2009) 0.98
Towards in silico lead optimization: scores from ensembles of protein/ligand conformations reliably correlate with biological activity. Proteins (2007) 0.94
Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring. J Chem Inf Comput Sci (2004) 0.93
Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. J Mol Recognit (2010) 0.93
Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization. Proteins (1998) 0.92
Molecular recognition and drug-lead identification: what can molecular simulations tell us? Curr Med Chem (2010) 0.91
Replica exchange molecular dynamics method for protein folding simulation. Methods Mol Biol (2007) 0.90
Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach. Protein Sci (2003) 0.89
Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design. Chem Biol Drug Des (2006) 0.88
HIV-reverse transcriptase inhibition: inclusion of ligand-induced fit by cross-docking studies. J Med Chem (2005) 0.88
A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. Comput Biol Chem (2009) 0.87
Protein structures in virtual screening: a case study with CDK2. J Med Chem (2006) 0.86
Potential drug-like inhibitors of Group 1 influenza neuraminidase identified through computer-aided drug design. Comput Biol Chem (2010) 0.84
Computational identification of uncharacterized cruzain binding sites. PLoS Negl Trop Dis (2010) 0.83
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res (2004) 11.53
Molecular dynamics simulations of biomolecules. Nat Struct Biol (2002) 7.68
Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J (2004) 6.67
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys (2004) 5.00
Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics (2006) 4.44
Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev (2006) 3.18
Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J (2004) 2.69
Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc (2002) 2.58
Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem (2004) 2.43
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci (2004) 2.34
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16
Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc Natl Acad Sci U S A (2006) 2.15
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Generalized Born model with a simple, robust molecular volume correction. J Chem Theory Comput (2007) 2.10
Discovery of a novel binding trench in HIV integrase. J Med Chem (2004) 2.09
A novel switch region regulates H-ras membrane orientation and signal output. EMBO J (2008) 2.06
Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc (2004) 2.00
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J Chem Phys (2007) 1.93
Molecular dynamics simulations and drug discovery. BMC Biol (2011) 1.91
Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer. J Med Chem (2007) 1.84
Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence. J Biol Chem (2004) 1.81
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers (2003) 1.80
POVME: an algorithm for measuring binding-pocket volumes. J Mol Graph Model (2010) 1.75
Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Structure (2008) 1.75
Application of the level-set method to the implicit solvation of nonpolar molecules. J Chem Phys (2007) 1.73
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei. Proc Natl Acad Sci U S A (2008) 1.73
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des (2008) 1.69
Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A (2012) 1.69
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol (2009) 1.67
A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A (2005) 1.66
Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc (2007) 1.65
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput (2012) 1.65
Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput Biol (2006) 1.65
Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J Mol Biol (2005) 1.64
Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model (2008) 1.64
Water in cavity-ligand recognition. J Am Chem Soc (2010) 1.63
Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. J Am Chem Soc (2002) 1.63
Exploring global motions and correlations in the ribosome. Biophys J (2005) 1.62
Toward a unified representation of protein structural dynamics in solution. J Am Chem Soc (2009) 1.55
Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. J Chem Theory Comput (2008) 1.52
How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study. J Am Chem Soc (2005) 1.51
Control of cation permeation through the nicotinic receptor channel. PLoS Comput Biol (2008) 1.51
Electrostatic free energy and its variations in implicit solvent models. J Phys Chem B (2008) 1.45
How Can Hydrophobic Association Be Enthalpy Driven? J Chem Theory Comput (2010) 1.44
Implementation of Accelerated Molecular Dynamics in NAMD. Comput Sci Discov (2011) 1.44
Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J Chem Phys (2007) 1.43
The physical basis of microtubule structure and stability. Protein Sci (2003) 1.43
Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys J (2006) 1.42
Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A (2013) 1.41
Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc (2009) 1.40
Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol (2010) 1.38
Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment. J Biol Chem (2005) 1.37
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res (2006) 1.37
The influence of macromolecular crowding on HIV-1 protease internal dynamics. J Am Chem Soc (2006) 1.37
Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J (2004) 1.35
Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys Chem Chem Phys (2011) 1.35
Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A (2012) 1.33
Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J Chem Phys (2005) 1.31
Limitations of atom-centered dielectric functions in implicit solvent models. J Phys Chem B (2005) 1.31
Potent, selective pyrone-based inhibitors of stromelysin-1. J Am Chem Soc (2005) 1.28
Molecular dynamics of acetylcholinesterase. Acc Chem Res (2002) 1.28
Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor. Biophys J (2007) 1.28
Ribosome motions modulate electrostatic properties. Biopolymers (2004) 1.27
Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective. J Mol Biol (2009) 1.27
Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol (2012) 1.26
Multiple pathways guide oxygen diffusion into flavoenzyme active sites. Proc Natl Acad Sci U S A (2009) 1.25
Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach. Chem Biol Drug Des (2010) 1.24
Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules. J Chem Theory Comput (2009) 1.23
Numerical analysis of Ca2+ signaling in rat ventricular myocytes with realistic transverse-axial tubular geometry and inhibited sarcoplasmic reticulum. PLoS Comput Biol (2010) 1.23
Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. J Am Chem Soc (2005) 1.23
Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophys J (2003) 1.23
Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach. J Chem Phys (2009) 1.22
Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations. J Mol Biol (2009) 1.21
NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. J Chem Inf Model (2010) 1.21
Calculating pKa values in enzyme active sites. Protein Sci (2003) 1.21
Novel allosteric sites on Ras for lead generation. PLoS One (2011) 1.20
Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach. J Am Chem Soc (2002) 1.20
Conformational selection in G-proteins: lessons from Ras and Rho. Biophys J (2010) 1.20
A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol (2010) 1.19
Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family. J Am Chem Soc (2007) 1.19
Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. J Am Chem Soc (2005) 1.19
Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J (2007) 1.18
Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers (2004) 1.18
Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc (2010) 1.18
Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation. J Am Chem Soc (2002) 1.17
Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain. J Mol Biol (2007) 1.17
Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain. Biophys J (2005) 1.17
Asymmetric structural motions of the homomeric alpha7 nicotinic receptor ligand binding domain revealed by molecular dynamics simulation. Biophys J (2003) 1.17
Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol (2006) 1.17
On the evaluation and optimization of protein X-ray structures for pKa calculations. Protein Sci (2003) 1.17
Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics. PLoS Comput Biol (2011) 1.16
Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2. J Am Chem Soc (2004) 1.16
H-ras protein in a bilayer: interaction and structure perturbation. J Am Chem Soc (2007) 1.16
Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain. J Am Chem Soc (2006) 1.15
Towards an in vivo biologically inspired nanofactory. Nat Nanotechnol (2007) 1.15
Structural and dynamic properties of water around acetylcholinesterase. Protein Sci (2002) 1.15
Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry (2011) 1.14
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A (2007) 1.14
Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design. Biopolymers (2006) 1.14
Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance. Biochemistry (2009) 1.14