Published in Phys Rev E Stat Nonlin Soft Matter Phys on February 02, 2011
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
Principal components of the protein dynamical transition. Phys Rev Lett (2003) 1.43
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
Nonergodicity mimics inhomogeneity in single particle tracking. Phys Rev Lett (2008) 1.20
Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities. Biophys J (2005) 1.19
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
Continuous-time random walk with correlated waiting times. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 1.12
Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. Biophys J (2005) 1.10
Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. Biophys J (2002) 1.09
The alpha helix dipole: screened out? Structure (2005) 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
Key role of electrostatic interactions in bacteriorhodopsin proton transfer. J Am Chem Soc (2004) 1.00
Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophys J (2012) 1.00
Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism. Biochemistry (2006) 0.99
Neutron frequency windows and the protein dynamical transition. Biophys J (2004) 0.98
Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns. Proteins (2007) 0.98
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
Optimal foraging by zooplankton within patches: the case of Daphnia. Math Biosci (2007) 0.97
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
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
Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke. J Mol Biol (2006) 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
Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study. Biophys J (2003) 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
Reversible dewetting of a molecularly thin fluid water film in a soft graphene-mica slit pore. Nano Lett (2012) 0.91
Elastic and conformational softness of a globular protein. Phys Rev Lett (2013) 0.90
Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water. Proteins (2005) 0.90
Spread of infectious diseases in directed and modular metapopulation networks. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.90
Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS. PLoS One (2010) 0.89
Langevin model of the temperature and hydration dependence of protein vibrational dynamics. J Phys Chem B (2005) 0.89
Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation. Phys Rev Lett (2005) 0.89
Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains. PLoS Comput Biol (2010) 0.89
Detection of individual p53-autoantibodies by using quenched peptide-based molecular probes. Angew Chem Int Ed Engl (2002) 0.89
Magnesium-dependent active-site conformational selection in the Diels-Alderase ribozyme. J Am Chem Soc (2010) 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
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
Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP. Biophys J (2012) 0.88
Structure and conformational dynamics of the metalloregulator MerR upon binding of Hg(II). J Mol Biol (2010) 0.87
Bulk-mediated diffusion on a planar surface: full solution. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 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
Bulk-mediated surface diffusion along a cylinder: Propagators and crossovers. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.87
Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease. Proteins (2003) 0.86
Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation. Biophys J (2012) 0.86
Conformational heterogeneity and low-frequency vibrational modes of proteins. Phys Chem Chem Phys (2006) 0.85
Effective surface motion on a reactive cylinder of particles that perform intermittent bulk diffusion. J Chem Phys (2011) 0.85
Test for determining a subdiffusive model in ergodic systems from single trajectories. Phys Rev Lett (2013) 0.85
Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching. J Comput Chem (2003) 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 dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution. Biophys J (2003) 0.85
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
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
Vibrational softening of a protein on ligand binding. J Phys Chem B (2011) 0.84
Methyl group dynamics and the onset of anharmonicity in myoglobin. J Phys Chem B (2008) 0.84
Subdiffusion of mixed origins: when ergodicity and nonergodicity coexist. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.83