Published in J Comput Chem on April 30, 2009
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Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput (2012) 3.40
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
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Taming the complexity of protein folding. Curr Opin Struct Biol (2011) 1.35
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Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. J Comput Aided Mol Des (2013) 0.87
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Folding Proteins at 500 ns/hour with Work Queue. Proc IEEE Int Conf Escience (2012) 0.78
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Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. Biochim Biophys Acta (2016) 0.77
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Computer-aided Drug Design: Using Numbers to your Advantage. ACS Med Chem Lett (2013) 0.77
Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units. J Chem Theory Comput (2012) 0.77
MSMBuilder: Statistical Models for Biomolecular Dynamics. Biophys J (2017) 0.76
Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs). J Comput Chem (2011) 0.76
Redesigning protein cavities as a strategy for increasing affinity in protein-protein interaction: interferon- γ receptor 1 as a model. Biomed Res Int (2015) 0.76
Modeling molecular kinetics with tICA and the kernel trick. J Chem Theory Comput (2015) 0.76
Long Timestep Molecular Dynamics on the Graphical Processing Unit. J Chem Theory Comput (2013) 0.75
Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides. J Comput Chem (2017) 0.75
The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid. J Comput Chem (2017) 0.75
GPU-Accelerated Molecular Dynamics Simulation to Study Liquid Crystal Phase Transition Using Coarse-Grained Gay-Berne Anisotropic Potential. PLoS One (2016) 0.75
Caseoperoxidase, mixed β-casein-SDS-hemin-imidazole complex: a nano artificial enzyme. J Biomol Struct Dyn (2015) 0.75
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Experimental tests of villin subdomain folding simulations. J Mol Biol (2003) 3.08
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
An experimental survey of the transition between two-state and downhill protein folding scenarios. Proc Natl Acad Sci U S A (2008) 2.57
Folding lambda-repressor at its speed limit. Biophys J (2004) 2.44
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Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys (2007) 4.52
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Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol (2002) 2.73
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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
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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
Structural basis for isozyme-specific regulation of electron transfer in nitric-oxide synthase. J Biol Chem (2004) 2.28
Protein folded states are kinetic hubs. Proc Natl Acad Sci U S A (2010) 2.27
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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
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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
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Error analysis and efficient sampling in Markovian state models for molecular dynamics. J Chem Phys (2005) 1.70
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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
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Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion. Proc Natl Acad Sci U S A (2006) 1.48
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Structural insight into RNA hairpin folding intermediates. J Am Chem Soc (2008) 1.39
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SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUs. J Chem Inf Model (2010) 1.21
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Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. J Am Chem Soc (2012) 1.19
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Unfolded-state dynamics and structure of protein L characterized by simulation and experiment. J Am Chem Soc (2010) 1.18
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Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments. Proc Natl Acad Sci U S A (2011) 1.14
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Simulated tempering yields insight into the low-resolution Rosetta scoring functions. Proteins (2009) 1.04