Published in J Chem Phys on May 22, 2004
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins (2010) 9.43
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B (2008) 4.68
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J (2005) 4.26
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc Natl Acad Sci U S A (2005) 4.15
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J Phys Chem B (2009) 3.17
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res (2009) 2.20
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements. J Chem Theory Comput (2012) 1.68
Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. Biophys J (2009) 1.61
Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. J Chem Theory Comput (2011) 1.55
Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proc Natl Acad Sci U S A (2009) 1.52
Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J Chem Phys (2012) 1.47
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association. J Chem Theory Comput (2014) 1.47
Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations. J Am Chem Soc (2008) 1.47
Charge asymmetries in hydration of polar solutes. J Phys Chem B (2008) 1.45
Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. J Comput Aided Mol Des (2010) 1.39
Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys (2012) 1.39
Ion pairing in molecular simulations of aqueous alkali halide solutions. J Phys Chem B (2009) 1.35
Systematic improvement of a classical molecular model of water. J Phys Chem B (2013) 1.31
Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. J Chem Theory Comput (2007) 1.28
Computational methods for biomolecular electrostatics. Methods Cell Biol (2008) 1.27
Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters. J Phys Chem B (2009) 1.25
Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. J Mol Biol (2010) 1.23
The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des (2014) 1.20
Homogeneous and heterogeneous tertiary structure ensembles of amyloid-β peptides. Biochemistry (2011) 1.19
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences. Proteins (2011) 1.16
Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J Chem Theory Comput (2013) 1.16
Exploring solvent effects upon the Menshutkin reaction using a polarizable force field. J Phys Chem B (2010) 1.15
Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations. J Comput Chem (2011) 1.14
Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions. Biointerphases (2008) 1.14
Small-angle scattering and the structure of ambient liquid water. Proc Natl Acad Sci U S A (2010) 1.13
Theory for the three-dimensional Mercedes-Benz model of water. J Chem Phys (2009) 1.12
Differences in β-strand populations of monomeric Aβ40 and Aβ42. Biophys J (2013) 1.08
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput (2014) 1.08
Alchemical prediction of hydration free energies for SAMPL. J Comput Aided Mol Des (2011) 1.07
Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization. J Phys Chem B (2013) 1.07
Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation. Proc Natl Acad Sci U S A (2013) 1.05
Intrinsic disorder modulates protein self-assembly and aggregation. Proc Natl Acad Sci U S A (2012) 1.05
The influence of protein dynamics on the success of computational enzyme design. J Am Chem Soc (2009) 1.04
Multipole electrostatics in hydration free energy calculations. J Comput Chem (2010) 1.00
Classical electrostatics for biomolecular simulations. Chem Rev (2013) 1.00
Ion counting from explicit-solvent simulations and 3D-RISM. Biophys J (2014) 0.99
Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data. Biophys J (2014) 0.98
Quantitative cw Overhauser effect dynamic nuclear polarization for the analysis of local water dynamics. Prog Nucl Magn Reson Spectrosc (2013) 0.98
The conformational ensembles of α-synuclein and tau: combining single-molecule FRET and simulations. Biophys J (2012) 0.98
A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration. J Phys Chem B (2014) 0.98
Temperature and pressure dependence of the optimized soft-sticky dipole-quadrupole-octupole water model. J Chem Phys (2010) 0.96
Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models. J Chem Phys (2012) 0.95
Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol (2010) 0.95
Dynamic architecture of a protein kinase. Proc Natl Acad Sci U S A (2014) 0.94
A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations. J Chem Theory Comput (2012) 0.94
Incorporating Phase-Dependent Polarizability in Non-Additive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid-Vapor Interface. J Chem Theory Comput (2009) 0.94
Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization. J Chem Theory Comput (2011) 0.93
Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions. J Chem Phys (2013) 0.93
Simple liquid models with corrected dielectric constants. J Phys Chem B (2012) 0.92
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model. J Phys Chem B (2015) 0.92
Building Water Models: A Different Approach. J Phys Chem Lett (2014) 0.91
Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid. J Chem Theory Comput (2009) 0.91
Properties of water along the liquid-vapor coexistence curve via molecular dynamics simulations using the polarizable TIP4P-QDP-LJ water model. J Chem Phys (2009) 0.91
The marine cyanobacterial metabolite gallinamide A is a potent and selective inhibitor of human cathepsin L. J Nat Prod (2013) 0.91
Molecular simulations of RNA 2'-O-transesterification reaction models in solution. J Phys Chem B (2012) 0.90
Six-site polarizable model of water based on the classical Drude oscillator. J Chem Phys (2013) 0.90
Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3. J Biomol NMR (2009) 0.90
TIP5P-Consistent Treatment of Electrostatics for Biomolecular Simulations. J Chem Theory Comput (2007) 0.89
A coarse-grained model of DNA with explicit solvation by water and ions. J Phys Chem B (2010) 0.89
Construction, MD simulation, and hydrodynamic validation of an all-atom model of a monoclonal IgG antibody. Biophys J (2010) 0.88
The large quadrupole of water molecules. J Chem Phys (2011) 0.88
The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. FEBS J (2014) 0.88
Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies. J Chem Theory Comput (2014) 0.88
Evaluating the strength of salt bridges: a comparison of current biomolecular force fields. J Phys Chem B (2014) 0.88
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins. J Chem Theory Comput (2014) 0.88
Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions. J Chem Theory Comput (2014) 0.87
Entropy from state probabilities: hydration entropy of cations. J Phys Chem B (2013) 0.87
Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes. J Phys Chem B (2012) 0.87
Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation. J Am Chem Soc (2016) 0.87
Solvation of Glucose, Trehalose, and Sucrose by the Soft Sticky Dipole-Quadrupole-Octupole Water Model. Chem Phys Lett (2010) 0.87
Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins. PLoS Comput Biol (2013) 0.86
Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation. J Phys Chem B (2010) 0.85
Structural dynamics and conformational equilibria of SERCA regulatory proteins in membranes by solid-state NMR restrained simulations. Biophys J (2014) 0.85
Multipolar Ewald methods, 1: theory, accuracy, and performance. J Chem Theory Comput (2015) 0.85
Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions. Chem Rev (2016) 0.84
The crystal structure of the streptococcal collagen-like protein 2 globular domain from invasive M3-type group A Streptococcus shows significant similarity to immunomodulatory HIV protein gp41. J Biol Chem (2013) 0.84
Distal loop flexibility of a regulatory domain modulates dynamics and activity of C-terminal SRC kinase (csk). PLoS Comput Biol (2013) 0.84
Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment. J Chem Theory Comput (2015) 0.84
Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path. J Am Chem Soc (2014) 0.84
pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study. J Phys Chem B (2013) 0.84
Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin. RNA (2015) 0.84
Multipolar Ewald methods, 2: applications using a quantum mechanical force field. J Chem Theory Comput (2015) 0.83
Sodium perchlorate effects on the helical stability of a mainly alanine peptide. Biophys J (2010) 0.83
Molecular dynamics simulation of triclinic lysozyme in a crystal lattice. Protein Sci (2015) 0.83
Unraveling cellulose microfibrils: a twisted tale. Biopolymers (2013) 0.83
Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other. J Chem Theory Comput (2013) 0.83
Nonadditive empirical force fields for short-chain linear alcohols: methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models. J Phys Chem B (2010) 0.82
Local order in the unfolded state: conformational biases and nearest neighbor interactions. Biomolecules (2014) 0.82
Towards a rational spacer design for bivalent inhibition of estrogen receptor. J Comput Aided Mol Des (2011) 0.82
Fascaplysin as a specific inhibitor for CDK4: insights from molecular modelling. PLoS One (2012) 0.82
Temperature dependence of the DNA double helix at the nanoscale: structure, elasticity, and fluctuations. Biophys J (2013) 0.82
Strength of hydrogen bonds of water depends on local environment. J Chem Phys (2012) 0.82
Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change. J Chem Theory Comput (2011) 0.82
Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations. Biochemistry (2015) 0.82
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys (2007) 9.07
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys (2007) 4.52
Structure and flexibility within proteins as identified through small angle X-ray scattering. Gen Physiol Biophys (2009) 3.24
Current status of the AMOEBA polarizable force field. J Phys Chem B (2010) 3.06
A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell (2006) 2.23
Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex. J Biol Chem (2009) 1.91
The structure and conformation of Lys63-linked tetraubiquitin. J Mol Biol (2009) 1.77
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. J Appl Crystallogr (2013) 1.69
Three-dimensional structure of the KChIP1-Kv4.3 T1 complex reveals a cross-shaped octamer. Nat Struct Mol Biol (2006) 1.64
Crosstalk between primase subunits can act to regulate primer synthesis in trans. Mol Cell (2005) 1.57
Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations. J Am Chem Soc (2008) 1.47
Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment. J Mol Biol (2004) 1.46
Structures of inactive retinoblastoma protein reveal multiple mechanisms for cell cycle control. Genes Dev (2012) 1.37
Coarse-grained sequences for protein folding and design. Proc Natl Acad Sci U S A (2003) 1.35
Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis. J Mol Biol (2008) 1.32
Systematic improvement of a classical molecular model of water. J Phys Chem B (2013) 1.31
Comprehensive macromolecular conformations mapped by quantitative SAXS analyses. Nat Methods (2013) 1.29
Dopamine transporter comparative molecular modeling and binding site prediction using the LeuT(Aa) leucine transporter as a template. Proteins (2008) 1.29
Optimizing solute-water van der Waals interactions to reproduce solvation free energies. J Phys Chem B (2012) 1.25
Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide. J Mol Biol (2006) 1.23
High-throughput SAXS for the characterization of biomolecules in solution: a practical approach. Methods Mol Biol (2014) 1.22
Hydration dynamics near a model protein surface. Biophys J (2004) 1.21
Structural analysis of flexible proteins in solution by small angle X-ray scattering combined with crystallography. J Struct Biol (2006) 1.21
Conformational trapping of mismatch recognition complex MSH2/MSH3 on repair-resistant DNA loops. Proc Natl Acad Sci U S A (2011) 1.21
Homogeneous and heterogeneous tertiary structure ensembles of amyloid-β peptides. Biochemistry (2011) 1.19
Crystal structure of the bifunctional proline utilization A flavoenzyme from Bradyrhizobium japonicum. Proc Natl Acad Sci U S A (2010) 1.16
Intermediates and the folding of proteins L and G. Protein Sci (2004) 1.13
Small-angle scattering and the structure of ambient liquid water. Proc Natl Acad Sci U S A (2010) 1.13
Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide. J Chem Phys (2006) 1.11
Differences in β-strand populations of monomeric Aβ40 and Aβ42. Biophys J (2013) 1.08
Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. J Chem Phys (2011) 1.08
Alchemical prediction of hydration free energies for SAMPL. J Comput Aided Mol Des (2011) 1.07
Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization. J Phys Chem B (2013) 1.07
Structural basis of guanine nucleotide exchange mediated by the T-cell essential Vav1. J Mol Biol (2008) 1.05
Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase. J Am Chem Soc (2005) 1.05
The influence of protein dynamics on the success of computational enzyme design. J Am Chem Soc (2009) 1.04
Observation of noncooperative folding thermodynamics in simulations of 1BBL. Biophys J (2008) 1.04
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
Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system. J Synchrotron Radiat (2010) 1.03
Soft patchy nanoparticles from solution-phase self-assembly of binary diblock copolymers. Nano Lett (2008) 1.03
An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research. Biotechnol Prog (2006) 1.02
Toward minimalist models of larger proteins: a ubiquitin-like protein. Proteins (2002) 1.01
Contrasting disease and nondisease protein aggregation by molecular simulation. Acc Chem Res (2008) 1.01
Antifreeze proteins at the ice/water interface: three calculated discriminating properties for orientation of type I proteins. Biophys J (2007) 1.00
Characterization of the TIP4P-Ew water model: vapor pressure and boiling point. J Chem Phys (2005) 1.00
Structure of the noncatalytic domains and global fold of the protein disulfide isomerase ERp72. Structure (2009) 1.00
Cool walking: a new Markov chain Monte Carlo sampling method. J Comput Chem (2003) 0.99
Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design. Proteins (2006) 0.98
Protein engineering study of protein L by simulation. J Comput Biol (2002) 0.98
Molecular dynamics of leucine and dopamine transporter proteins in a model cell membrane lipid bilayer. Proteins (2010) 0.97
Modeling chemical bonding effects for protein electron crystallography: the transferable fragmental electrostatic potential (TFESP) method. Acta Crystallogr A (2002) 0.97
Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase. Biophys J (2013) 0.96
Structural and dynamic implications of an effector-induced backbone amide cis-trans isomerization in cytochrome P450cam. J Mol Biol (2009) 0.96
Influence of denatured and intermediate states of folding on protein aggregation. Protein Sci (2005) 0.95
Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol (2010) 0.95
Crystal structure of the unliganded retinoblastoma protein pocket domain. Proteins (2011) 0.94
The reaction mechanism for the organocatalytic ring-opening polymerization of l-lactide using a guanidine-based catalyst: hydrogen-bonded or covalently bound? J Am Chem Soc (2008) 0.93
Salt dependence of an alpha-helical peptide folding energy landscapes. Biochemistry (2009) 0.93
Family 18 chitinase-oligosaccharide substrate interaction: subsite preference and anomer selectivity of Serratia marcescens chitinase A. Biochem J (2003) 0.93
Molecular view of water dynamics near model peptides. J Phys Chem B (2005) 0.92
Hydrophobic potential of mean force as a solvation function for protein structure prediction. Structure (2007) 0.91
Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions. Biophys J (2010) 0.91
Representability problems for coarse-grained water potentials. J Chem Phys (2007) 0.91
Reducing lambda repressor to the core. J Phys Chem B (2011) 0.91
LeuT conformational sampling utilizing accelerated molecular dynamics and principal component analysis. Biophys J (2012) 0.90
Effects of co-solvents on peptide hydration water structure and dynamics. Phys Chem Chem Phys (2009) 0.90
Protofibril assemblies of the arctic, Dutch, and Flemish mutants of the Alzheimer's Abeta1-40 peptide. Biophys J (2007) 0.89
Comparison of structure determination methods for intrinsically disordered amyloid-β peptides. J Phys Chem B (2014) 0.89
Methods for applying the quantitative structure-activity relationship paradigm. Methods Mol Biol (2004) 0.89
Monoamine transporter structure, function, dynamics, and drug discovery: a computational perspective. AAPS J (2012) 0.89
A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding. Proteins (2008) 0.88
A New and Efficient Poisson-Boltzmann Solver for Interaction of Multiple Proteins. J Chem Theory Comput (2010) 0.87
Kinetic computational alanine scanning: application to p53 oligomerization. J Mol Biol (2006) 0.86
Hydration water dynamics near biological interfaces. J Phys Chem B (2009) 0.86
Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm. J Chem Inf Model (2008) 0.86
Kinetic and docking studies of the interaction of quinones with the quinone reductase active site. Biochemistry (2003) 0.86
Experimentally restrained molecular dynamics simulations for characterizing the open states of cytochrome P450cam. Biochemistry (2011) 0.85
Evolution of the potential energy landscape with static pulling force for two model proteins. J Phys Chem B (2012) 0.85
Two-dimensional pattern formation using graphoepitaxy of PS-b-PMMA block copolymers for advanced FinFET device and circuit fabrication. ACS Nano (2014) 0.85
Structure and water dynamics of aqueous peptide solutions in the presence of co-solvents. Phys Chem Chem Phys (2009) 0.84
How hot? Systematic convergence of the replica exchange method using multiple reservoirs. J Comput Chem (2010) 0.84
Relative free energy of binding and binding mode calculations of HIV-1 RT inhibitors based on dock-MM-PB/GS. Proteins (2004) 0.84
Aqueous peptides as experimental models for hydration water dynamics near protein surfaces. Phys Chem Chem Phys (2008) 0.84
Family 18 chitolectins: comparison of MGP40 and HUMGP39. Biochem Biophys Res Commun (2007) 0.84
Reliable protein structure refinement using a physical energy function. J Comput Chem (2010) 0.83
Insights from molecular dynamics: the binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters. J Mol Graph Model (2012) 0.83
CoMFA 3D-QSAR analysis of HIV-1 RT nonnucleoside inhibitors, TIBO derivatives based on docking conformation and alignment. J Chem Inf Comput Sci (2004) 0.83
Sodium perchlorate effects on the helical stability of a mainly alanine peptide. Biophys J (2010) 0.83
Advanced potential energy surfaces for condensed phase simulation. Annu Rev Phys Chem (2013) 0.82
Small-angle X-ray scattering studies of the oligomeric state and quaternary structure of the trifunctional proline utilization A (PutA) flavoprotein from Escherichia coli. J Biol Chem (2011) 0.82
Separable cooperative and localized translational motions of water confined by a chemically heterogeneous environment. Phys Chem Chem Phys (2007) 0.82
Structural and functional characterization of CalS11, a TDP-rhamnose 3'-O-methyltransferase involved in calicheamicin biosynthesis. ACS Chem Biol (2013) 0.82
Structure, dynamics, and specificity of endoglucanase D from Clostridium cellulovorans. J Mol Biol (2013) 0.82
Benchmarking docking and scoring protocol for the identification of potential acetylcholinesterase inhibitors. J Mol Graph Model (2010) 0.82
A physical approach to protein structure prediction. Biophys J (2002) 0.81
Single particle and collective hydration dynamics for hydrophobic and hydrophilic peptides. J Chem Phys (2007) 0.81