Published in Methods Mol Biol on January 01, 2008
Dynamic allostery in the methionine repressor revealed by force distribution analysis. PLoS Comput Biol (2009) 1.21
MAVENs: motion analysis and visualization of elastic networks and structural ensembles. BMC Bioinformatics (2011) 1.16
Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning. PLoS Comput Biol (2011) 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
Molecular mechanism of misfolding and aggregation of Aβ(13-23). J Phys Chem B (2013) 1.01
Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study. PLoS One (2012) 0.96
Structural transitions and energy landscape for Cowpea Chlorotic Mottle Virus capsid mechanics from nanomanipulation in vitro and in silico. Biophys J (2013) 0.93
Molecular mechanisms, thermodynamics, and dissociation kinetics of knob-hole interactions in fibrin. J Biol Chem (2013) 0.87
Soft-assembled Multilevel Dynamics of Tactical Behaviors in Soccer. Front Psychol (2016) 0.85
Principal component and clustering analysis on molecular dynamics data of the ribosomal L11·23S subdomain. J Mol Model (2012) 0.83
Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics. BMC Genomics (2014) 0.81
Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure. F1000 Biol Rep (2009) 0.81
Finding semirigid domains in biomolecules by clustering pair-distance variations. Biomed Res Int (2014) 0.79
Elastic network models capture the motions apparent within ensembles of RNA structures. RNA (2014) 0.79
Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase. Sci Rep (2017) 0.78
An investigation of G-quadruplex structural polymorphism in the human telomere using a combined approach of hydrodynamic bead modeling and molecular dynamics simulation. J Phys Chem B (2014) 0.78
Distributions of experimental protein structures on coarse-grained free energy landscapes. J Chem Phys (2015) 0.78
Optimal superpositioning of flexible molecule ensembles. Biophys J (2013) 0.77
Sulfamethoxazole induces a switch mechanism in T cell receptors containing TCRVβ20-1, altering pHLA recognition. PLoS One (2013) 0.77
AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis. BMC Bioinformatics (2015) 0.76
Functional and Structural Analyses of CYP1B1 Variants Linked to Congenital and Adult-Onset Glaucoma to Investigate the Molecular Basis of These Diseases. PLoS One (2016) 0.76
Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations. Nat Commun (2016) 0.76
Early Events in the Amyloid Formation of the A546T Mutant of Transforming Growth Factor β-Induced Protein in Corneal Dystrophies Compared to the Nonfibrillating R555W and R555Q Mutants. Biochemistry (2015) 0.75
Computational study of the activity, dynamics, energetics and conformations of insulin analogues using molecular dynamics simulations: Application to hyperinsulinemia and the critical residue B26. Biochem Biophys Rep (2017) 0.75
On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase. Sci Rep (2017) 0.75
Rational design of novel, fluorescent, tagged glutamic acid dendrimers with different terminal groups and in silico analysis of their properties. Int J Nanomedicine (2017) 0.75
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (2008) 8.04
Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J Comput Aided Mol Des (2010) 2.67
Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles. EMBO J (2006) 2.19
Predicting free energy changes using structural ensembles. Nat Methods (2009) 1.93
Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys J (2010) 1.75
Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci U S A (2008) 1.67
Structure and function of water channels. Curr Opin Struct Biol (2002) 1.55
Quaternary ammonium compounds as water channel blockers. Specificity, potency, and site of action. J Biol Chem (2006) 1.46
Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations. Biophys J (2008) 1.43
Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism. PLoS Biol (2009) 1.41
Protein thermostability calculations using alchemical free energy simulations. Biophys J (2010) 1.33
Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. J Biomol NMR (2008) 1.33
Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophys J (2011) 1.30
Does CO2 permeate through aquaporin-1? Biophys J (2006) 1.28
Detection of functional modes in protein dynamics. PLoS Comput Biol (2009) 1.27
Geometry-based sampling of conformational transitions in proteins. Structure (2007) 1.26
Speeding up parallel GROMACS on high-latency networks. J Comput Chem (2007) 1.23
Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments. Eur Biophys J (2007) 1.14
Functional dynamics in the voltage-dependent anion channel. Proc Natl Acad Sci U S A (2010) 1.13
Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. Structures of complexes with the substrate. J Biol Chem (2002) 1.13
Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p. J Mol Biol (2008) 1.09
Short-range order and collective dynamics of DMPC bilayers: a comparison between molecular dynamics simulations, X-ray, and neutron scattering experiments. Biophys J (2007) 1.07
Kinetics of conformational sampling in ubiquitin. Angew Chem Int Ed Engl (2011) 1.07
Alternative splicing of SNAP-25 regulates secretion through nonconservative substitutions in the SNARE domain. Mol Biol Cell (2005) 1.06
Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes. Biophys J (2009) 1.06
Aquaporin-9 protein is the primary route of hepatocyte glycerol uptake for glycerol gluconeogenesis in mice. J Biol Chem (2011) 1.04
Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection. PLoS Comput Biol (2012) 1.04
β-Barrel mobility underlies closure of the voltage-dependent anion channel. Structure (2012) 1.04
The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study. Structure (2008) 1.03
Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? Handb Exp Pharmacol (2009) 1.02
Voltage-regulated water flux through aquaporin channels in silico. Biophys J (2010) 1.01
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PLoS Comput Biol (2010) 1.01
Determinants of water permeability through nanoscopic hydrophilic channels. Biophys J (2009) 1.01
Molecular driving forces defining lipid positions around aquaporin-0. Proc Natl Acad Sci U S A (2012) 0.99
Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes. J Am Chem Soc (2010) 0.97
Mobility of a one-dimensional confined file of water molecules as a function of file length. Phys Rev Lett (2006) 0.95
Toward a consensus model of the HERG potassium channel. ChemMedChem (2010) 0.95
Partial least-squares functional mode analysis: application to the membrane proteins AQP1, Aqy1, and CLC-ec1. Biophys J (2012) 0.94
The 4.5 A structure of human AQP2. J Mol Biol (2005) 0.94
Computational analysis of local membrane properties. J Comput Aided Mol Des (2013) 0.94
A designed conformational shift to control protein binding specificity. Angew Chem Int Ed Engl (2014) 0.93
The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation. Structure (2008) 0.92
Discovery of novel human aquaporin-1 blockers. ACS Chem Biol (2012) 0.92
Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions. Angew Chem Int Ed Engl (2005) 0.91
Population shuffling of protein conformations. Angew Chem Int Ed Engl (2014) 0.91
Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proc Natl Acad Sci U S A (2013) 0.91
Invariance of single-file water mobility in gramicidin-like peptidic pores as function of pore length. Biophys J (2007) 0.90
Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochem Soc Trans (2008) 0.90
Is TEA an inhibitor for human Aquaporin-1? Pflugers Arch (2008) 0.90
Driving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations. J Mol Biol (2012) 0.88
Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin. Phys Chem Chem Phys (2010) 0.88
Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation. PLoS Comput Biol (2010) 0.86
Towards computational specificity screening of DNA-binding proteins. Nucleic Acids Res (2011) 0.85
The identification of novel, high affinity AQP9 inhibitors in an intracellular binding site. Mol Membr Biol (2013) 0.85
pmx: Automated protein structure and topology generation for alchemical perturbations. J Comput Chem (2014) 0.84
Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange. Biophys J (2007) 0.84
Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps. Proteins (2007) 0.84
Ligand-release pathways in the pheromone-binding protein of Bombyx mori. Structure (2006) 0.83
Phosphorylation of rat aquaporin-4 at Ser(111) is not required for channel gating. Glia (2013) 0.83
Computer simulations of structure-activity relationships for HERG channel blockers. Biochemistry (2011) 0.82
Mapping the conformational dynamics and pathways of spontaneous steric zipper Peptide oligomerization. PLoS One (2011) 0.82
Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys J (2005) 0.81
Alternate structural conformations of Streptococcus pneumoniae hyaluronan lyase: insights into enzyme flexibility and underlying molecular mechanism of action. J Mol Biol (2006) 0.81
Probing the energy landscape of activation gating of the bacterial potassium channel KcsA. PLoS Comput Biol (2013) 0.81
A molecular switch driving inactivation in the cardiac K+ channel HERG. PLoS One (2012) 0.81
Binding of glutamate to the umami receptor. Biophys Chem (2010) 0.80
Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels. Biophys J (2012) 0.80
Not only enthalpy: large entropy contribution to ion permeation barriers in single-file channels. Biophys J (2008) 0.79
The thermodynamic influence of trapped water molecules on a protein-ligand interaction. Angew Chem Int Ed Engl (2009) 0.79
Spontaneous aggregation of the insulin-derived steric zipper peptide VEALYL results in different aggregation forms with common features. J Mol Biol (2014) 0.79
Domain motions of hyaluronan lyase underlying processive hyaluronan translocation. Proteins (2009) 0.79
Collective dynamics underlying allosteric transitions in hemoglobin. PLoS Comput Biol (2013) 0.79
Optimal superpositioning of flexible molecule ensembles. Biophys J (2013) 0.77
Identification of selective inhibitors of the potassium channel Kv1.1-1.2((3)) by high-throughput virtual screening and automated patch clamp. ChemMedChem (2012) 0.77
How the dynamics of the metal-binding loop region controls the acid transition in cupredoxins. Biochemistry (2013) 0.76
Calculation of binding free energies. Methods Mol Biol (2015) 0.76
Comment on "Molecular selectivity in aquaporin channels studied by the 3D-RISM theory". J Phys Chem B (2011) 0.75
Molecular dynamics in principal component space. J Phys Chem B (2012) 0.75
Alchemical free energy calculations for nucleotide mutations in protein-DNA complexes. J Chem Theory Comput (2017) 0.75