Published in J Mol Biol on October 21, 2005
Are current molecular dynamics force fields too helical? Biophys J (2008) 3.13
Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions. Proc Natl Acad Sci U S A (2006) 2.00
Long single alpha-helical tail domains bridge the gap between structure and function of myosin VI. Nat Struct Mol Biol (2008) 1.88
Dynamic charge interactions create surprising rigidity in the ER/K alpha-helical protein motif. Proc Natl Acad Sci U S A (2008) 1.50
Solution conformation and thermodynamic characteristics of RNA binding by the splicing factor U2AF65. J Biol Chem (2008) 1.03
Harnessing the unique structural properties of isolated α-helices. J Biol Chem (2014) 0.94
Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains. J Chem Theory Comput (2012) 0.90
Surface-sensitive Raman spectroscopy of collagen I fibrils. Biophys J (2011) 0.89
Conformation of a peptide encompassing the proton translocation channel of vacuolar H(+)-ATPase. Biophys J (2006) 0.79
Molecular dynamics simulations of the folding of poly(alanine) peptides. J Mol Model (2011) 0.78
Structural basis of folding cooperativity in model proteins: insights from a microcanonical perspective. Biophys J (2011) 0.76
Interplay between adsorbed peptide structure, trapped water, and surface hydrophobicity. Biointerphases (2017) 0.75
Dimeric and Trimeric Fusion Proteins Generated with Fimbrial Adhesins of Uropathogenic Escherichia coli. Front Cell Infect Microbiol (2016) 0.75
Molecular dynamics simulation and conformational analysis of some catalytically active peptides. J Mol Model (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
Exploring the folding landscape of a structured RNA. Proc Natl Acad Sci U S A (2001) 2.78
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
Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu Rev Biophys Biomol Struct (2007) 2.36
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
Rapid compaction during RNA folding. Proc Natl Acad Sci U S A (2002) 2.27
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
Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. J Am Chem Soc (2007) 2.20
Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J Mol Biol (2006) 2.19
A comparative study of motor-protein motions by using a simple elastic-network model. Proc Natl Acad Sci U S A (2003) 2.17
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
Biophysical properties of the synucleins and their propensities to fibrillate: inhibition of alpha-synuclein assembly by beta- and gamma-synucleins. J Biol Chem (2002) 2.07
Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis. Cell (2003) 2.02
Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. Adv Protein Chem (2002) 2.02
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
Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J Mol Biol (2004) 1.90
Direct calculation of the binding free energies of FKBP ligands. J Chem Phys (2005) 1.88
Long single alpha-helical tail domains bridge the gap between structure and function of myosin VI. Nat Struct Mol Biol (2008) 1.88
The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. J Mol Biol (2003) 1.80
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
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure (2005) 1.60
Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory. Biophys J (2007) 1.60
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
Dynamic charge interactions create surprising rigidity in the ER/K alpha-helical protein motif. Proc Natl Acad Sci U S A (2008) 1.50
Size and shape of detergent micelles determined by small-angle X-ray scattering. J Phys Chem B (2007) 1.49
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
Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proc Natl Acad Sci U S A (2005) 1.46
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
Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques. J Mol Biol (2002) 1.41
Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy. Proc Natl Acad Sci U S A (2004) 1.39
Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Sci (2002) 1.39
Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophys J (2003) 1.39
The ligand-free state of the TPP riboswitch: a partially folded RNA structure. J Mol Biol (2009) 1.39
Structural insight into RNA hairpin folding intermediates. J Am Chem Soc (2008) 1.39
Partially folded intermediates in insulin fibrillation. Biochemistry (2003) 1.38
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
The complete VS ribozyme in solution studied by small-angle X-ray scattering. Structure (2008) 1.34
Nuclear localization of alpha-synuclein and its interaction with histones. Biochemistry (2003) 1.33
MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. Nucleic Acids Res (2007) 1.32
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