Published in Pac Symp Biocomput on January 01, 2009
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Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. J Chem Phys (2006) 1.27
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Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. J Am Chem Soc (2008) 1.26
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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
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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
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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
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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