Published in J Comput Chem on April 30, 2010
Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains. J Phys Chem B (2011) 0.99
Coarse-grained force field: general folding theory. Phys Chem Chem Phys (2011) 0.99
Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains. J Phys Chem B (2011) 0.95
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
Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine. J Chem Theory Comput (2012) 0.84
Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. J Chem Theory Comput (2012) 0.82
Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations. J Chem Theory Comput (2015) 0.79
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Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode. J Phys Chem B (2005) 1.71
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Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems. J Phys Chem B (2005) 1.69
A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proc Natl Acad Sci U S A (2002) 1.64
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Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation. Proc Natl Acad Sci U S A (2009) 1.59
Predicting 13Calpha chemical shifts for validation of protein structures. J Biomol NMR (2007) 1.59
Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH. J Mol Biol (2004) 1.58
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Principal component analysis for protein folding dynamics. J Mol Biol (2008) 1.42
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Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures. Proc Natl Acad Sci U S A (2003) 1.40
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Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field. J Chem Theory Comput (2006) 1.27
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Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains. J Mol Biol (2005) 1.25
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems. J Phys Chem B (2007) 1.23
Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. J Comput Chem (2009) 1.22
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A (2010) 1.19
Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins. J Chem Theory Comput (2009) 1.19
Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method. J Comput Chem (2002) 1.15
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains. J Phys Chem B (2008) 1.15
Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures. Proteins (2008) 1.14
Sequential nearest-neighbor effects on computed 13Calpha chemical shifts. J Biomol NMR (2010) 1.14
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Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts. Acc Chem Res (2009) 1.11
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A new force field (ECEPP-05) for peptides, proteins, and organic molecules. J Phys Chem B (2006) 1.10
Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function. J Chem Phys (2006) 1.08
An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics. J Phys Chem B (2009) 1.08
beta-hairpin-forming peptides; models of early stages of protein folding. Biophys Chem (2010) 1.07
Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH. Proc Natl Acad Sci U S A (2011) 1.07
How main-chains of proteins explore the free-energy landscape in native states. Proc Natl Acad Sci U S A (2008) 1.06
Use of 13Calpha chemical shifts in protein structure determination. J Phys Chem B (2007) 1.04
Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field. J Mol Biol (2010) 1.04
Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent. J Comput Chem (2007) 1.02
Packing helices in proteins by global optimization of a potential energy function. Proc Natl Acad Sci U S A (2003) 1.00
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Further evidence for the absence of polyproline II stretch in the XAO peptide. Biophys J (2007) 1.00
Performance of density functional models to reproduce observed (13)C(alpha) chemical shifts of proteins in solution. J Comput Chem (2009) 0.99
Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains. J Phys Chem B (2011) 0.99
Coarse-grained force field: general folding theory. Phys Chem Chem Phys (2011) 0.99
Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles. Biophys Chem (2003) 0.99
How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics? Phys Rev Lett (2009) 0.99
Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein. J Am Chem Soc (2010) 0.98
What can we learn by computing 13Calpha chemical shifts for X-ray protein models? Acta Crystallogr D Biol Crystallogr (2009) 0.98
Use of 13C(alpha) chemical shifts for accurate determination of beta-sheet structures in solution. Proc Natl Acad Sci U S A (2008) 0.98
Dissimilarity in the reductive unfolding pathways of two ribonuclease homologues. J Mol Biol (2004) 0.96
Relation between free energy landscapes of proteins and dynamics. J Chem Theory Comput (2010) 0.96
On the orientation of the backbone dipoles in native folds. Proc Natl Acad Sci U S A (2005) 0.96
Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains. J Phys Chem B (2011) 0.95
Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds. Protein Eng Des Sel (2004) 0.95
Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy. J Phys Chem B (2007) 0.94
Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate. Biopolymers (2003) 0.93
Potential of mean force of hydrophobic association: dependence on solute size. J Phys Chem B (2007) 0.93
Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins. J Phys Chem B (2007) 0.92
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets. Proc Natl Acad Sci U S A (2013) 0.92