How well can simulation predict protein folding kinetics and thermodynamics?

Protein folding studied by single-molecule FRET. Curr Opin Struct Biol (2008) 4.33

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

Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories. Proc Natl Acad Sci U S A (2009) 2.29

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

P versus Q: structural reaction coordinates capture protein folding on smooth landscapes. Proc Natl Acad Sci U S A (2006) 2.01

Deformation and failure of protein materials in physiologically extreme conditions and disease. Nat Mater (2009) 2.00

Early events in protein folding explored by rapid mixing methods. Chem Rev (2006) 1.50

Protein folding under confinement: a role for solvent. Proc Natl Acad Sci U S A (2007) 1.30

Kinetic definition of protein folding transition state ensembles and reaction coordinates. Biophys J (2006) 1.25

A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL. Biophys J (2006) 1.20

Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci U S A (2006) 1.19

Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopy. Nat Commun (2012) 1.13

Choreographing an enzyme's dance. Curr Opin Chem Biol (2010) 1.10

Dominant folding pathways of a WW domain. Proc Natl Acad Sci U S A (2012) 1.07

Modeling the self-assembly of the cellulosome enzyme complex. J Biol Chem (2010) 1.05

Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel. Biophys J (2008) 1.03

Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. Proc Natl Acad Sci U S A (2010) 1.02

Gating mechanisms of mechanosensitive channels of large conductance, I: a continuum mechanics-based hierarchical framework. Biophys J (2008) 1.01

Design of protein-ligand binding based on the molecular-mechanics energy model. J Mol Biol (2008) 1.01

Making connections between ultrafast protein folding kinetics and molecular dynamics simulations. Proc Natl Acad Sci U S A (2011) 1.00

Predicting peptide structures in native proteins from physical simulations of fragments. PLoS Comput Biol (2009) 0.98

Dynamics of lysozyme structure network: probing the process of unfolding. Biophys J (2007) 0.97

Polarizable atomic multipole X-ray refinement: application to peptide crystals. Acta Crystallogr D Biol Crystallogr (2009) 0.97

Reaching the protein folding speed limit with large, sub-microsecond pressure jumps. Nat Methods (2009) 0.96

Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model. J Chem Theory Comput (2012) 0.96

The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe. Biophys J (2010) 0.96

Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics. J Phys Chem B (2009) 0.96

Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations. Biophys J (2006) 0.91

Microsecond folding experiments and simulations: a match is made. Phys Chem Chem Phys (2013) 0.91

Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics. J Chem Theory Comput (2010) 0.89

Structure and stability of the lamin A tail domain and HGPS mutant. J Struct Biol (2011) 0.87

Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition. Br J Pharmacol (2009) 0.85

Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J (2015) 0.83

Protein folding in a reverse micelle environment: the role of confinement and dehydration. J Chem Phys (2011) 0.82

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. J Comput Aided Mol Des (2014) 0.81

Geofold: topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability. Proteins (2011) 0.80

Computational design and experimental discovery of an antiestrogenic peptide derived from alpha-fetoprotein. J Am Chem Soc (2007) 0.79

A second look at mini-protein stability: analysis of FSD-1 using circular dichroism, differential scanning calorimetry, and simulations. Biophys J (2009) 0.79

How fast does a signal propagate through proteins? PLoS One (2013) 0.79

An information theoretic approach to macromolecular modeling: II. Force fields. Biophys J (2005) 0.79

Multiple replica repulsion technique for efficient conformational sampling of biological systems. Biophys J (2011) 0.78

Downhill protein folding under pressure. Nat Methods (2009) 0.77

Fast in silico protein folding by introduction of alternating hydrogen bond potentials. Biophys J (2008) 0.77

Equilibrium sampling for biomolecules under mechanical tension. Biophys J (2010) 0.77

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity. Front Mol Biosci (2015) 0.77

Structural dynamics and inhibitor searching for Wnt-4 protein using comparative computational studies. Drug Des Devel Ther (2015) 0.76

Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation. Int J Mol Sci (2009) 0.76

Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape. Biophys J (2016) 0.76

Reliable protein folding on complex energy landscapes: the free energy reaction path. Biophys J (2008) 0.75

NUMERICAL SIMULATION OF NANOINDENTATION AND PATCH CLAMP EXPERIMENTS ON MECHANOSENSITIVE CHANNELS OF LARGE CONDUCTANCE IN ESCHERICHIA COLI. Shi Yan Li Xue (2009) 0.75

Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation. F1000Res (2015) 0.75

Advances in methods and algorithms in a modern quantum chemistry program package. Phys Chem Chem Phys (2006) 6.51

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

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers (2003) 2.35

Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science (2006) 2.32

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

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

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

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

Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics. Nucleic Acids Res (2010) 1.14

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

Increased detection of structural templates using alignments of designed sequences. Proteins (2003) 1.07

Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories. J Comput Chem (2008) 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