Error analysis and efficient sampling in Markovian state models for molecular dynamics.

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

Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol (2011) 2.31

Everything you wanted to know about Markov State Models but were afraid to ask. Methods (2010) 2.24

To milliseconds and beyond: challenges in the simulation of protein folding. Curr Opin Struct Biol (2012) 1.77

Rapid equilibrium sampling initiated from nonequilibrium data. Proc Natl Acad Sci U S A (2009) 1.54

Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin. Proc Natl Acad Sci U S A (2007) 1.50

Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nat Commun (2014) 1.48

Src kinase conformational activation: thermodynamics, pathways, and mechanisms. PLoS Comput Biol (2008) 1.43

Enhanced modeling via network theory: Adaptive sampling of Markov state models. J Chem Theory Comput (2010) 1.37

Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages. J Chem Phys (2009) 1.31

Building Markov state models along pathways to determine free energies and rates of transitions. J Chem Phys (2008) 1.18

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint. J Chem Phys (2009) 1.08

Using Markov models to simulate electron spin resonance spectra from molecular dynamics trajectories. J Phys Chem B (2008) 1.05

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

Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics. PLoS Comput Biol (2007) 1.03

Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach. J Chem Phys (2008) 1.02

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models. Nat Commun (2015) 0.99

Maximum Flux Transition Paths of Conformational Change. J Chem Theory Comput (2010) 0.98

Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations. MAbs (2013) 0.89

NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. J Phys Chem B (2013) 0.87

Characterization and rapid sampling of protein folding Markov state model topologies. J Chem Theory Comput (2011) 0.86

Allostery through the computational microscope: cAMP activation of a canonical signalling domain. Nat Commun (2015) 0.85

Perspective: Markov models for long-timescale biomolecular dynamics. J Chem Phys (2014) 0.85

Computational models of protein kinematics and dynamics: beyond simulation. Annu Rev Anal Chem (Palo Alto Calif) (2012) 0.84

AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble. J Chem Inf Model (2014) 0.83

Protein folding is mechanistically robust. Biophys J (2012) 0.82

Persistent topology and metastable state in conformational dynamics. PLoS One (2013) 0.78

Quantitative analysis of ligand migration from transition networks. Biophys J (2010) 0.78

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol (2016) 0.78

Beating the millisecond barrier in molecular dynamics simulations. Biophys J (2015) 0.76

Multiensemble Markov models of molecular thermodynamics and kinetics. Proc Natl Acad Sci U S A (2016) 0.76

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions. J Chem Phys (2014) 0.75

Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4-protein interaction. Phys Chem Chem Phys (2015) 0.75

A comparison of weighted ensemble and Markov state model methodologies. J Chem Phys (2015) 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

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. J Chem Phys (2005) 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

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

Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics. J Chem Phys (2007) 1.53

Assessment of the protein-structure refinement category in CASP8. Proteins (2009) 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

Topological methods for exploring low-density states in biomolecular folding pathways. J Chem Phys (2009) 1.10

Bayesian detection of intensity changes in single molecule and molecular dynamics trajectories. J Phys Chem B (2010) 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

A role for confined water in chaperonin function. J Am Chem Soc (2008) 1.06

Network models for molecular kinetics and their initial applications to human health. Cell Res (2010) 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

Foldamer dynamics expressed via Markov state models. II. State space decomposition. J Chem Phys (2005) 1.03

Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics. PLoS Comput Biol (2007) 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

Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms. Pac Symp Biocomput (2010) 0.99