Published in Phys Rev Lett on November 14, 2003
Principal component analysis for protein folding dynamics. J Mol Biol (2008) 1.42
Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. Biophys J (2007) 1.30
Influence of hydration on the dynamics of lysozyme. Biophys J (2006) 1.27
Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps. Proc Natl Acad Sci U S A (2009) 1.08
The dynamical transition of proteins, concepts and misconceptions. Eur Biophys J (2008) 1.00
Neutron frequency windows and the protein dynamical transition. Biophys J (2004) 0.98
Computational identification of slow conformational fluctuations in proteins. J Phys Chem B (2009) 0.96
Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation. Proc Natl Acad Sci U S A (2007) 0.94
Enzyme activity and flexibility at very low hydration. Biophys J (2005) 0.91
Interfacial water at protein surfaces: wide-line NMR and DSC characterization of hydration in ubiquitin solutions. Biophys J (2009) 0.90
Structure, dynamics and reactions of protein hydration water. Philos Trans R Soc Lond B Biol Sci (2004) 0.89
Structural and dynamical examination of the low-temperature glass transition in serum albumin. Biophys J (2006) 0.89
Correlated motions and interactions at the onset of the DNA-induced partial unfolding of Ets-1. Biophys J (2009) 0.89
Functional domain motions in proteins on the ~1-100 ns timescale: comparison of neutron spin-echo spectroscopy of phosphoglycerate kinase with molecular-dynamics simulation. Biophys J (2012) 0.88
Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins. Prion (2011) 0.87
Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer. J Phys Chem B (2008) 0.87
The pathway of oligomeric DNA melting investigated by molecular dynamics simulations. Biophys J (2008) 0.85
Influence of water clustering on the dynamics of hydration water at the surface of a lysozyme. Biophys J (2007) 0.84
Slowdown of Interhelical Motions Induces a Glass Transition in RNA. Biophys J (2015) 0.82
Zaccai neutron resilience and site-specific hydration dynamics in a globular protein. Eur Phys J E Soft Matter (2013) 0.81
Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra. Biophys J (2008) 0.81
An experimental and computational investigation of spontaneous lasso formation in microcin J25. Biophys J (2010) 0.81
A structural mechanism for calcium transporter headpiece closure. J Phys Chem B (2015) 0.81
Mechanism of displacement of a catalytically essential loop from the active site of mammalian fructose-1,6-bisphosphatase. Biochemistry (2013) 0.78
Water molecule contributions to proton spin-lattice relaxation in rotationally immobilized proteins. J Magn Reson (2009) 0.78
Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution. Evol Appl (2015) 0.77
ADLD: a novel graphical representation of protein sequences and its application. Comput Math Methods Med (2014) 0.75
Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters. PLoS Comput Biol (2014) 0.75
Instantaneous normal modes and the protein glass transition. Biophys J (2009) 0.75
Shape-Dependent Global Deformation Modes of Large Protein Structures. J Mol Struct (2010) 0.75
Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin. J Mol Model (2014) 0.75
Interacting mechanism of ID3 HLH domain towards E2A/E12 transcription factor - An Insight through molecular dynamics and docking approach. Biochem Biophys Rep (2015) 0.75
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (2013) 11.01
The genetic basis for bacterial mercury methylation. Science (2013) 2.87
Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states. J Chem Phys (2007) 2.23
Is the first hydration shell of lysozyme of higher density than bulk water? Proc Natl Acad Sci U S A (2002) 2.19
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc Natl Acad Sci U S A (2011) 1.96
Structural mechanism of the recovery stroke in the myosin molecular motor. Proc Natl Acad Sci U S A (2005) 1.66
Translational hydration water dynamics drives the protein glass transition. Biophys J (2003) 1.63
Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation. J Am Chem Soc (2003) 1.42
SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins. Acta Crystallogr D Biol Crystallogr (2002) 1.36
Structural basis of cellulosome efficiency explored by small angle X-ray scattering. J Biol Chem (2005) 1.32
Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. Biophys J (2007) 1.30
Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations. J Am Chem Soc (2008) 1.30
Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2010) 1.26
The structural coupling between ATPase activation and recovery stroke in the myosin II motor. Structure (2007) 1.22
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? J Comput Chem (2002) 1.21
In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions. J Am Chem Soc (2011) 1.20
Direct determination of vibrational density of states change on ligand binding to a protein. Phys Rev Lett (2004) 1.20
Mechanism of primary proton transfer in bacteriorhodopsin. Structure (2004) 1.17
Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21. Proteins (2005) 1.12
Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. Biophys J (2005) 1.10
The alpha helix dipole: screened out? Structure (2005) 1.09
Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. Biophys J (2002) 1.09
Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides. J Am Chem Soc (2010) 1.09
The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor. J Mol Biol (2006) 1.08
Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proc Natl Acad Sci U S A (2007) 1.07
Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study. J Phys Chem B (2007) 1.05
Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics. J Phys Chem B (2005) 1.05
Role of histone tails in structural stability of the nucleosome. PLoS Comput Biol (2011) 1.04
Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog. Biotechnol Biofuels (2012) 1.04
A molecular mechanics force field for biologically important sterols. J Comput Chem (2005) 1.03
Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. J Chem Phys (2011) 1.03
Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophys J (2012) 1.00
Key role of electrostatic interactions in bacteriorhodopsin proton transfer. J Am Chem Soc (2004) 1.00
Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism. Biochemistry (2006) 0.99
Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. J Comput Chem (2010) 0.98
Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns. Proteins (2007) 0.98
Neutron frequency windows and the protein dynamical transition. Biophys J (2004) 0.98
Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.96
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc Natl Acad Sci U S A (2011) 0.96
Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. J Am Chem Soc (2009) 0.95
Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke. J Mol Biol (2006) 0.95
Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering. Biophys J (2008) 0.95
Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein. J Am Chem Soc (2012) 0.95
Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations. Biophys J (2012) 0.94
Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation. Proc Natl Acad Sci U S A (2007) 0.94
Lattice dynamics of a protein crystal. Phys Rev Lett (2007) 0.93
Simulation analysis of the temperature dependence of lignin structure and dynamics. J Am Chem Soc (2011) 0.93
Peptide partitioning properties from direct insertion studies. Biophys J (2010) 0.92
Structural characterization of intramolecular Hg(2+) transfer between flexibly linked domains of mercuric ion reductase. J Mol Biol (2011) 0.92
Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions. J Phys Chem B (2008) 0.91
Small angle neutron scattering reveals pH-dependent conformational changes in Trichoderma reesei cellobiohydrolase I: implications for enzymatic activity. J Biol Chem (2011) 0.91
Enzyme activity and flexibility at very low hydration. Biophys J (2005) 0.91
Elastic and conformational softness of a globular protein. Phys Rev Lett (2013) 0.90
Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS. PLoS One (2010) 0.89
Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation. Phys Rev Lett (2005) 0.89
Langevin model of the temperature and hydration dependence of protein vibrational dynamics. J Phys Chem B (2005) 0.89
Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains. PLoS Comput Biol (2010) 0.89
Magnesium-dependent active-site conformational selection in the Diels-Alderase ribozyme. J Am Chem Soc (2010) 0.89
Detection of individual p53-autoantibodies by using quenched peptide-based molecular probes. Angew Chem Int Ed Engl (2002) 0.89
Charge-based interactions between peptides observed as the dominant force for association in aqueous solution. Angew Chem Int Ed Engl (2008) 0.89
Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: a quantum mechanical/molecular mechanical analysis. Biochemistry (2009) 0.88
Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP. Biophys J (2012) 0.88
Structural modeling and molecular dynamics simulation of the actin filament. Proteins (2011) 0.88
Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein. Phys Rev Lett (2011) 0.88
Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k. J Am Chem Soc (2006) 0.88
Structure and conformational dynamics of the metalloregulator MerR upon binding of Hg(II). J Mol Biol (2010) 0.87
Radical coupling reactions in lignin synthesis: a density functional theory study. J Phys Chem B (2012) 0.87
Subdiffusion in peptides originates from the fractal-like structure of configuration space. Phys Rev Lett (2008) 0.87
Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation. Biophys J (2012) 0.86
Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease. Proteins (2003) 0.86
Conformational heterogeneity and low-frequency vibrational modes of proteins. Phys Chem Chem Phys (2006) 0.85
The dynamic transition in proteins may have a simple explanation. Faraday Discuss (2003) 0.85
Understanding the energetics of helical peptide orientation in membranes. Proteins (2005) 0.85
Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching. J Comput Chem (2003) 0.85
Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution. Biophys J (2003) 0.85
Methyl group dynamics and the onset of anharmonicity in myoglobin. J Phys Chem B (2008) 0.84
Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state. Proteins (2009) 0.84
Pressure-dependent transition in protein dynamics at about revealed by molecular dynamics simulation. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.84
Vibrational softening of a protein on ligand binding. J Phys Chem B (2011) 0.84
Long-distance proton transfer with a break in the bacteriorhodopsin active site. J Am Chem Soc (2009) 0.84
Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps. J Phys Chem B (2005) 0.84
Increase of both order and disorder in the first hydration shell with increasing solute polarity. Phys Rev Lett (2011) 0.83
REACH coarse-grained simulation of a cellulose fiber. Biomacromolecules (2012) 0.83
Water pathways in the bacteriorhodopsin proton pump. J Membr Biol (2010) 0.83
Mechanism of Hg-C protonolysis in the organomercurial lyase MerB. J Am Chem Soc (2009) 0.83
Solvent-driven preferential association of lignin with regions of crystalline cellulose in molecular dynamics simulation. Biomacromolecules (2013) 0.83
Energy triplets for writing epigenetic marks: insights from QM/MM free-energy simulations of protein lysine methyltransferases. Chemistry (2009) 0.82
Derivation of mean-square displacements for protein dynamics from elastic incoherent neutron scattering. J Phys Chem B (2012) 0.82
Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.82
Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping. Proteins (2006) 0.82
Subdiffusion in time-averaged, confined random walks. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.82
Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core. Phys Rev Lett (2012) 0.82
Mechanism of a molecular valve in the halorhodopsin chloride pump. Structure (2005) 0.82
Coarse-grain model for natural cellulose fibrils in explicit water. J Phys Chem B (2014) 0.82
A molecular mechanics force field for lignin. J Comput Chem (2009) 0.82
Zaccai neutron resilience and site-specific hydration dynamics in a globular protein. Eur Phys J E Soft Matter (2013) 0.81
X-ray structure of a Hg2+ complex of mercuric reductase (MerA) and quantum mechanical/molecular mechanical study of Hg2+ transfer between the C-terminal and buried catalytic site cysteine pairs. Biochemistry (2014) 0.81
VinaMPI: facilitating multiple receptor high-throughput virtual docking on high-performance computers. J Comput Chem (2013) 0.81
Molecular modeling of O6-methylguanine-DNA methyltransferase mutant proteins encoded by single nucleotide polymorphisms. Int J Mol Med (2005) 0.81
REACH coarse-grained normal mode analysis of protein dimer interaction dynamics. Biophys J (2009) 0.81