Published in Proc Natl Acad Sci U S A on January 26, 2005
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc (2006) 2.59
Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophys J (2008) 1.82
Protein folding by zipping and assembly. Proc Natl Acad Sci U S A (2007) 1.72
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
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
Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proc Natl Acad Sci U S A (2005) 1.65
Two-stage folding of HP-35 from ab initio simulations. J Mol Biol (2007) 1.59
Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol (2008) 1.54
The effect of long-range interactions on the secondary structure formation of proteins. Protein Sci (2005) 1.47
Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field. J Chem Theory Comput (2006) 1.27
Folding pathway of the b1 domain of protein G explored by multiscale modeling. Biophys J (2007) 1.25
Mimicking the folding pathway to improve homology-free protein structure prediction. Proc Natl Acad Sci U S A (2009) 1.25
Characterization of protein-folding pathways by reduced-space modeling. Proc Natl Acad Sci U S A (2007) 1.24
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
Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci U S A (2006) 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
Protein folding requires crowd control in a simulated cell. J Mol Biol (2010) 1.18
Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins. Nucleic Acids Res (2006) 1.11
Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility. Proteins (2012) 1.11
The energy computation paradox and ab initio protein folding. PLoS One (2011) 1.10
High-resolution protein folding with a transferable potential. Proc Natl Acad Sci U S A (2005) 1.09
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
The power of coarse graining in biomolecular simulations. Wiley Interdiscip Rev Comput Mol Sci (2014) 1.00
Coarse-grained force field: general folding theory. Phys Chem Chem Phys (2011) 0.99
A force field for virtual atom molecular mechanics of proteins. Proc Natl Acad Sci U S A (2009) 0.99
Blind test of physics-based prediction of protein structures. Biophys J (2009) 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
Relation between free energy landscapes of proteins and dynamics. J Chem Theory Comput (2010) 0.96
Multiscale characterization of protein conformational ensembles. Proteins (2009) 0.95
Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins. J Phys Chem B (2007) 0.92
PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. J Mol Biol (2010) 0.91
De novo prediction of protein folding pathways and structure using the principle of sequential stabilization. Proc Natl Acad Sci U S A (2012) 0.91
Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. J Chem Theory Comput (2012) 0.91
PRIMO: A Transferable Coarse-grained Force Field for Proteins. J Chem Theory Comput (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
Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. Phys Rev Lett (2013) 0.88
A comparative study of the reported performance of ab initio protein structure prediction algorithms. J R Soc Interface (2008) 0.88
Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state. Proc Natl Acad Sci U S A (2012) 0.86
Putting the pathway back into protein folding. Proc Natl Acad Sci U S A (2005) 0.86
Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements. Proc Natl Acad Sci U S A (2014) 0.84
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
Local vs global motions in protein folding. J Chem Theory Comput (2013) 0.84
Hidden protein folding pathways in free-energy landscapes uncovered by network analysis. J Chem Theory Comput (2012) 0.83
Accounting for a mirror-image conformation as a subtle effect in protein folding. Proc Natl Acad Sci U S A (2014) 0.83
Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides. Proteins (2010) 0.83
Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations. Proc Natl Acad Sci U S A (2010) 0.83
Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. J Chem Theory Comput (2012) 0.82
Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain. J Chem Phys (2008) 0.81
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions. J Mol Model (2014) 0.81
Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states. J Chem Theory Comput (2013) 0.81
Folding and self-assembly of a small protein complex. J Chem Theory Comput (2012) 0.81
Use of decoys to optimize an all-atom force field including hydration. Biophys J (2008) 0.80
Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field. J Chem Theory Comput (2008) 0.80
Folding mechanism of β-hairpin trpzip2: heterogeneity, transition state and folding pathways. Int J Mol Sci (2009) 0.80
Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field. Proteins (2009) 0.80
From helix-coil transitions to protein folding. Biopolymers (2008) 0.79
First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids. Sci Data (2016) 0.79
REACH coarse-grained biomolecular simulation: transferability between different protein structural classes. Biophys J (2008) 0.79
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
Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches. Proteins (2015) 0.78
Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements. BMC Bioinformatics (2008) 0.78
Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions. J Chem Theory Comput (2015) 0.78
Kinks, loops, and protein folding, with protein A as an example. J Chem Phys (2014) 0.77
Folding and association of a homotetrameric protein complex in an all-atom Go model. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 0.77
Folding simulations of the A and B domains of protein G. J Phys Chem B (2012) 0.77
New Insights into Protein (Un)Folding Dynamics. J Phys Chem Lett (2015) 0.77
A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins. Proc Natl Acad Sci U S A (2009) 0.77
Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association. J Chem Theory Comput (2014) 0.77
Into the fold. Advances in technology and algorithms facilitate great strides in protein structure prediction. EMBO Rep (2006) 0.76
Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides. J Chem Theory Comput (2015) 0.76
Union of geometric constraint-based simulations with molecular dynamics for protein structure prediction. Biophys J (2010) 0.76
Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field. J Chem Theory Comput (2014) 0.76
Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field. J Mol Model (2015) 0.76
A generic force field for protein coarse-grained molecular dynamics simulation. Int J Mol Sci (2012) 0.76
Recent advances in transferable coarse-grained modeling of proteins. Adv Protein Chem Struct Biol (2014) 0.75
Folding and self-assembly of a small heterotetramer. J Chem Phys (2014) 0.75
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinformatics (2016) 0.75
TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates. Proteins (2010) 0.75
Energy Minimization of Discrete Protein Titration State Models Using Graph Theory. J Phys Chem B (2016) 0.75
Molecular Simulations Find Stable Structures in Fragments of Protein G. Acta Chim Slov (2008) 0.75
Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction. J Chem Phys (2016) 0.75
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Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach. J Chem Phys (2015) 0.75
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The protein folding problem: global optimization of the force fields. Front Biosci (2004) 1.09
Funnel sculpting for in silico assembly of secondary structure elements of proteins. Proc Natl Acad Sci U S A (2003) 1.02
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An atomically detailed study of the folding pathways of protein A with the stochastic difference equation. Proc Natl Acad Sci U S A (2002) 1.76
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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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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
Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. Proc Natl Acad Sci U S A (2006) 1.57
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Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol (2008) 1.54
Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. Proc Natl Acad Sci U S A (2008) 1.50
The role of hydrophobic interactions in initiation and propagation of protein folding. Proc Natl Acad Sci U S A (2006) 1.42
Principal component analysis for protein folding dynamics. J Mol Biol (2008) 1.42
Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test. Acta Crystallogr B (2011) 1.40
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
Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test. Acta Crystallogr B (2009) 1.29
Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry. Biochemistry (2006) 1.28
Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field. J Chem Theory Comput (2006) 1.27
Addition of side chains to a known backbone with defined side-chain centroids. Biophys Chem (2003) 1.27
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
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
Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method. J Comput Chem (2002) 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
Topology of Type II REases revisited; structural classes and the common conserved core. Nucleic Acids Res (2007) 1.11
Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts. Acc Chem Res (2009) 1.11
Polyproline II helix conformation in a proline-rich environment: a theoretical study. Biophys J (2004) 1.10
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
Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: a theoretical study. J Biomol NMR (2002) 1.00
Further evidence for the absence of polyproline II stretch in the XAO peptide. Biophys J (2007) 1.00
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
Performance of density functional models to reproduce observed (13)C(alpha) chemical shifts of proteins in solution. J Comput Chem (2009) 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
Potential of mean force of hydrophobic association: dependence on solute size. J Phys Chem B (2007) 0.93
Intramolecular versus intermolecular disulfide bonds in prion proteins. J Biol Chem (2002) 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
Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins. J Phys Chem B (2007) 0.92
Potential of mean force of association of large hydrophobic particles: toward the nanoscale limit. J Phys Chem B (2010) 0.92
PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. J Mol Biol (2010) 0.91
Influence of charge and size of terminal amino-acid residues on local conformational states and shape of alanine-based peptides. Biopolymers (2008) 0.91
Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. J Chem Theory Comput (2012) 0.91
Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin. Biochemistry (2004) 0.90
Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation. Proteins (2009) 0.90
Inhibitor design by wrapping packing defects in HIV-1 proteins. Proc Natl Acad Sci U S A (2004) 0.89
Unblocked statistical-coil tetrapeptides in aqueous solution: quantum-chemical computation of the carbon-13 NMR chemical shifts. J Biomol NMR (2003) 0.89
Characterization of the fast-forming intermediate, des [30-75], in the reductive unfolding of onconase. Biochemistry (2004) 0.89
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
FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins. J Phys Chem B (2008) 0.89
Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin-binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein. Biopolymers (2010) 0.88
WeFold: a coopetition for protein structure prediction. Proteins (2014) 0.88
Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. Phys Rev Lett (2013) 0.88
Ultrarapid mixing experiments shed new light on the characteristics of the initial conformational ensemble during the folding of ribonuclease A. Proc Natl Acad Sci U S A (2004) 0.87
Coarse-grained model of nucleic acid bases. J Comput Chem (2010) 0.86
Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures. Protein Eng Des Sel (2009) 0.86
CheShift-2: graphic validation of protein structures. Bioinformatics (2012) 0.86
Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain. J Mol Biol (2012) 0.86
Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state. Proc Natl Acad Sci U S A (2012) 0.86
Conformational propensities of protein folding intermediates: distribution of species in the 1S, 2S, and 3S ensembles of the [C40A,C95A] mutant of bovine pancreatic ribonuclease A. Biochemistry (2002) 0.86
A new method for rapid characterization of the folding pathways of multidisulfide-containing proteins. J Am Chem Soc (2004) 0.86
Analysis of 13Calpha and 13Cbeta chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach. J Biomol NMR (2010) 0.85
Coupling between conformation and proton binding in proteins. Proteins (2005) 0.85
Assessment of two theoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment. J Phys Chem B (2006) 0.85
Simultaneous characterization of the reductive unfolding pathways of RNase B isoforms by top-down mass spectrometry. Chem Biol (2004) 0.85