Published in J Mol Biol on August 26, 2011
Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). Eur Biophys J (2012) 1.13
The structure of the mercury transporter MerF in phospholipid bilayers: a large conformational rearrangement results from N-terminal truncation. J Am Chem Soc (2013) 0.92
Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering. Sci Adv (2016) 0.84
On the mechanism and rate of gold incorporation into thiol-dependent flavoreductases. J Inorg Biochem (2011) 0.83
Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase. Biophys J (2014) 0.82
Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinase function. PLoS Comput Biol (2012) 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
Dimerization and phosphatase activity of calcyclin-binding protein/Siah-1 interacting protein: the influence of oxidative stress. FASEB J (2015) 0.76
The development of solid-state NMR of membrane proteins. Biomed Spectrosc Imaging (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
Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol Rev (2003) 2.72
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
A qualitative study exploring moral distress in the ICU team: the importance of unit functionality and intrateam dynamics. Crit Care Med (2015) 1.51
Principal components of the protein dynamical transition. Phys Rev Lett (2003) 1.43
Written versus oral recommendations made by pharmacy students during internal medicine rotations. Ann Pharmacother (2007) 1.42
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
Kinetic buffering of cross talk between bacterial two-component sensors. J Mol Biol (2009) 1.32
The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun (2013) 1.32
Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations. J Am Chem Soc (2008) 1.30
Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. Biophys J (2007) 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
Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface. J Chem Phys (2008) 1.26
The structural coupling between ATPase activation and recovery stroke in the myosin II motor. Structure (2007) 1.22
A general protocol for the crystallization of membrane proteins for X-ray structural investigation. Nat Protoc (2009) 1.21
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
Quantitative identification of the protonation state of histidines in vitro and in vivo. Biochemistry (2003) 1.11
Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. Biophys J (2005) 1.10
The mechanism of inhibition of antibody-based inhibitors of membrane-type serine protease 1 (MT-SP1). J Mol Biol (2007) 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
Active transport, substrate specificity, and methylation of Hg(II) in anaerobic bacteria. Proc Natl Acad Sci U S A (2011) 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
Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry (2005) 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
NmerA, the metal binding domain of mercuric ion reductase, removes Hg2+ from proteins, delivers it to the catalytic core, and protects cells under glutathione-depleted conditions. Biochemistry (2005) 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
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
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
Kinetic controls on the complexation between mercury and dissolved organic matter in a contaminated environment. Environ Sci Technol (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
Mercury adaptation among bacteria from a deep-sea hydrothermal vent. Appl Environ Microbiol (2005) 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
Click dendrimers and triazole-related aspects: catalysts, mechanism, synthesis, and functions. A bridge between dendritic architectures and nanomaterials. Acc Chem Res (2011) 0.94
Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation. Proc Natl Acad Sci U S A (2007) 0.94
The X-ray crystal structure of Shewanella oneidensis OmcA reveals new insight at the microbe-mineral interface. FEBS Lett (2014) 0.93
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
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
Mercury reduction and complexation by natural organic matter in anoxic environments. Proc Natl Acad Sci U S A (2011) 0.89
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
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
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
Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k. J Am Chem Soc (2006) 0.88
Persistent cytomegalovirus-specific memory responses in the lung allograft and blood following primary infection in lung transplant recipients. J Immunol (2006) 0.88
Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein. Phys Rev Lett (2011) 0.88
Structure and conformational dynamics of the metalloregulator MerR upon binding of Hg(II). J Mol Biol (2010) 0.87
Hypoglycemia associated with the use of levofloxacin. Am J Health Syst Pharm (2009) 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
NmerA of Tn501 mercuric ion reductase: structural modulation of the pKa values of the metal binding cysteine thiols. Biochemistry (2010) 0.87
Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. Microb Ecol (2010) 0.86
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
Understanding the energetics of helical peptide orientation in membranes. Proteins (2005) 0.85