Insight into the role of hydration on protein dynamics.

Functionally important conformations of the Met20 loop in dihydrofolate reductase are populated by rapid thermal fluctuations. J Am Chem Soc (2009) 1.22

Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics. J Chem Theory Comput (2011) 1.05

Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophys J (2012) 1.00

Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozyme. RNA (2010) 0.98

A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw. Proc Natl Acad Sci U S A (2007) 0.94

Mechanistic insight into the role of transition-state stabilization in cyclophilin A. J Am Chem Soc (2009) 0.92

Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach. Biophys J (2008) 0.90

Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches. Biophys J (2014) 0.86

Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo. J Phys Chem B (2010) 0.85

Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J (2015) 0.83

Role of hydration in collagen recognition by bacterial adhesins. Biophys J (2011) 0.81

Normal-mode-analysis-guided investigation of crucial intersubunit contacts in the cAMP-dependent gating in HCN channels. Biophys J (2012) 0.78

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

Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog (2011) 1.57

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

Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. Proc Natl Acad Sci U S A (2005) 1.42

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

Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective. J Mol Biol (2009) 1.27

Ribosome motions modulate electrostatic properties. Biopolymers (2004) 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

Appreciating HIV type 1 diversity: subtype differences in Env. AIDS Res Hum Retroviruses (2009) 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

Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2. J Am Chem Soc (2004) 1.16

Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics. PLoS Comput Biol (2011) 1.16

H-ras protein in a bilayer: interaction and structure perturbation. J Am Chem Soc (2007) 1.16