Published in J Chem Phys on April 08, 2005
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
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Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys (2008) 3.87
Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol (2011) 2.31
Predicting absolute ligand binding free energies to a simple model site. J Mol Biol (2007) 2.19
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. J Chem Theory Comput (2012) 2.07
Molecular basis of the apparent near ideality of urea solutions. Biophys J (2007) 1.43
Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages. J Chem Phys (2009) 1.31
Backbone additivity in the transfer model of protein solvation. Protein Sci (2010) 1.13
Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Q Rev Biophys (2011) 1.12
Theory of binless multi-state free energy estimation with applications to protein-ligand binding. J Chem Phys (2012) 1.10
Peptide conformational preferences in osmolyte solutions: transfer free energies of decaalanine. J Am Chem Soc (2011) 1.09
Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins (2009) 1.08
Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods. J Biol Chem (2011) 1.03
Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations. J Chem Theory Comput (2010) 1.02
Protein-protein interaction investigated by steered molecular dynamics: the TCR-pMHC complex. Biophys J (2008) 1.00
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise. J Chem Phys (2008) 0.96
Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding. Curr Protein Pept Sci (2009) 0.95
Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations. J Chem Phys (2009) 0.94
A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations. J Chem Theory Comput (2012) 0.94
Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. J Comput Aided Mol Des (2014) 0.92
Solvation free energies of alanine peptides: the effect of flexibility. J Phys Chem B (2013) 0.91
Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes. J Chem Theory Comput (2014) 0.91
Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package. J Chem Theory Comput (2013) 0.88
Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation. J Comput Chem (2013) 0.86
Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. J Chem Theory Comput (2011) 0.86
From laptop to benchtop to bedside: structure-based drug design on protein targets. Curr Pharm Des (2012) 0.85
Separated topologies--a method for relative binding free energy calculations using orientational restraints. J Chem Phys (2013) 0.85
Structure-Based, Rational Design of T Cell Receptors. Front Immunol (2013) 0.84
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
Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization. J Comput Chem (2011) 0.82
Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration. Biophys J (2011) 0.79
A dynamic view of enzyme catalysis. J Mol Model (2008) 0.78
Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis. Front Mol Biosci (2015) 0.77
Computational study of evolutionary selection pressure on rainbow trout estrogen receptors. PLoS One (2010) 0.77
Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level. J Comput Chem (2016) 0.76
Accurate estimation of solvation free energy using polynomial fitting techniques. J Comput Chem (2011) 0.76
Structural perturbation of a dipalmitoylphosphatidylcholine (DPPC) bilayer by warfarin and its bolaamphiphilic analogue: A molecular dynamics study. J Colloid Interface Sci (2016) 0.76
The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations. Sci Rep (2016) 0.76
Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion. J Chem Phys (2014) 0.75
Effect of Oxidative Damage on the Stability and Dimerization of Superoxide Dismutase 1. Biophys J (2016) 0.75
Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches. J Comput Chem (2016) 0.75
Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. J Comput Chem (2017) 0.75
Absolute comparison of simulated and experimental protein-folding dynamics. Nature (2002) 5.68
Accelerating molecular dynamic simulation on graphics processing units. J Comput Chem (2009) 4.58
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys (2007) 4.52
Random-coil behavior and the dimensions of chemically unfolded proteins. Proc Natl Acad Sci U S A (2004) 4.44
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J (2005) 4.26
Multiplexed-replica exchange molecular dynamics method for protein folding simulation. Biophys J (2003) 3.35
Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J Am Chem Soc (2010) 3.18
Current status of the AMOEBA polarizable force field. J Phys Chem B (2010) 3.06
Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. J Mol Biol (2007) 2.77
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. J Chem Phys (2005) 2.76
Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol (2002) 2.73
Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys (2009) 2.64
Using generalized ensemble simulations and Markov state models to identify conformational states. Methods (2009) 2.60
Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science (2006) 2.32
Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol (2011) 2.31
Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. Phys Rev Lett (2003) 2.30
Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. J Chem Phys (2004) 2.30
Protein folded states are kinetic hubs. Proc Natl Acad Sci U S A (2010) 2.27
Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. J Med Chem (2008) 2.27
The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. J Am Chem Soc (2002) 2.26
Native-like mean structure in the unfolded ensemble of small proteins. J Mol Biol (2002) 2.23
Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. J Chem Phys (2006) 2.22
MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. J Chem Theory Comput (2011) 2.15
Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'. Nature (2012) 2.08
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. J Chem Theory Comput (2012) 2.07
How well can simulation predict protein folding kinetics and thermodynamics? Annu Rev Biophys Biomol Struct (2005) 1.98
Simulations of the role of water in the protein-folding mechanism. Proc Natl Acad Sci U S A (2004) 1.95
Atomistic folding simulations of the five-helix bundle protein λ(6−85). J Am Chem Soc (2011) 1.94
Direct calculation of the binding free energies of FKBP ligands. J Chem Phys (2005) 1.88
To milliseconds and beyond: challenges in the simulation of protein folding. Curr Opin Struct Biol (2012) 1.77
Error analysis and efficient sampling in Markovian state models for molecular dynamics. J Chem Phys (2005) 1.70
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements. J Chem Theory Comput (2012) 1.68
The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations. Biophys J (2009) 1.58
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J Comput Chem (2010) 1.55
Rapid equilibrium sampling initiated from nonequilibrium data. Proc Natl Acad Sci U S A (2009) 1.54
Markov state model reveals folding and functional dynamics in ultra-long MD trajectories. J Am Chem Soc (2011) 1.54
Assessment of the protein-structure refinement category in CASP8. Proteins (2009) 1.53
Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics. J Chem Phys (2007) 1.53
Can conformational change be described by only a few normal modes? Biophys J (2005) 1.53
Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling. J Comput Chem (2005) 1.51
Accurate and efficient corrections for missing dispersion interactions in molecular simulations. J Phys Chem B (2007) 1.49
Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion. Proc Natl Acad Sci U S A (2006) 1.48
RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. J Mol Biol (2002) 1.45
Simple few-state models reveal hidden complexity in protein folding. Proc Natl Acad Sci U S A (2012) 1.43
Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails. PLoS Comput Biol (2010) 1.42
Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15. Nat Immunol (2012) 1.41
Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy. Proc Natl Acad Sci U S A (2004) 1.39
Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophys J (2003) 1.39
Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Sci (2002) 1.39
Structural insight into RNA hairpin folding intermediates. J Am Chem Soc (2008) 1.39
Enhanced modeling via network theory: Adaptive sampling of Markov state models. J Chem Theory Comput (2010) 1.37
Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. J Chem Phys (2008) 1.36
Taming the complexity of protein folding. Curr Opin Struct Biol (2011) 1.35
Does water play a structural role in the folding of small nucleic acids? Biophys J (2005) 1.34
Systematic improvement of a classical molecular model of water. J Phys Chem B (2013) 1.31
Unusual compactness of a polyproline type II structure. Proc Natl Acad Sci U S A (2005) 1.30
Protein folding under confinement: a role for solvent. Proc Natl Acad Sci U S A (2007) 1.30
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9. J Chem Theory Comput (2013) 1.30
Does native state topology determine the RNA folding mechanism? J Mol Biol (2004) 1.30
Nanotube confinement denatures protein helices. J Am Chem Soc (2006) 1.29
Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. J Chem Phys (2006) 1.27
One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution. J Phys Chem B (2005) 1.27
Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. J Am Chem Soc (2008) 1.26
Normal mode partitioning of Langevin dynamics for biomolecules. J Chem Phys (2008) 1.26
Kinetic definition of protein folding transition state ensembles and reaction coordinates. Biophys J (2006) 1.25
The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation. J Mol Biol (2009) 1.24
Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water. J Chem Phys (2005) 1.23
Side-chain recognition and gating in the ribosome exit tunnel. Proc Natl Acad Sci U S A (2008) 1.23
Validation of Markov state models using Shannon's entropy. J Chem Phys (2006) 1.22
SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUs. J Chem Inf Model (2010) 1.21
The Simbios National Center: Systems Biology in Motion. Proc IEEE Inst Electr Electron Eng (2008) 1.20
Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. J Am Chem Soc (2012) 1.19
Do conformational biases of simple helical junctions influence RNA folding stability and specificity? RNA (2009) 1.19
Unfolded-state dynamics and structure of protein L characterized by simulation and experiment. J Am Chem Soc (2010) 1.18
How large is an alpha-helix? Studies of the radii of gyration of helical peptides by small-angle X-ray scattering and molecular dynamics. J Mol Biol (2005) 1.16
Bayesian update method for adaptive weighted sampling. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 1.16
Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties. Nat Struct Biol (2003) 1.15
Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments. Proc Natl Acad Sci U S A (2011) 1.14
Calculations of the electric fields in liquid solutions. J Phys Chem B (2013) 1.13
Bayesian detection of intensity changes in single molecule and molecular dynamics trajectories. J Phys Chem B (2010) 1.10
Topological methods for exploring low-density states in biomolecular folding pathways. J Chem Phys (2009) 1.10
A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides. J Comput Chem (2005) 1.09
Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. J Chem Phys (2011) 1.08
Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories. J Comput Chem (2008) 1.07
Increased detection of structural templates using alignments of designed sequences. Proteins (2003) 1.07
Network models for molecular kinetics and their initial applications to human health. Cell Res (2010) 1.06
A role for confined water in chaperonin function. J Am Chem Soc (2008) 1.06
Precursor directed biosynthesis of an orthogonally functional erythromycin analogue: selectivity in the ribosome macrolide binding pocket. J Am Chem Soc (2012) 1.06
Persistent voids: a new structural metric for membrane fusion. Bioinformatics (2007) 1.05
PAPER--accelerating parallel evaluations of ROCS. J Comput Chem (2010) 1.04
Simulated tempering yields insight into the low-resolution Rosetta scoring functions. Proteins (2009) 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
Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations. J Mol Biol (2005) 1.03
Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics. PLoS Comput Biol (2007) 1.03
Foldamer dynamics expressed via Markov state models. II. State space decomposition. J Chem Phys (2005) 1.03
Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer. Biophys J (2012) 1.02
Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach. J Chem Phys (2008) 1.02
SCISSORS: a linear-algebraical technique to rapidly approximate chemical similarities. J Chem Inf Model (2010) 1.01
CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations. J Chem Theory Comput (2010) 1.01