Published in J Phys Chem B on April 18, 2011
Coarse-grained force field: general folding theory. Phys Chem Chem Phys (2011) 0.99
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
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev (2014) 0.88
A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ(1-28)). J Phys Chem B (2011) 0.84
Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation. J Chem Theory Comput (2013) 0.83
Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. J Chem Theory Comput (2012) 0.82
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
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions. J Mol Model (2014) 0.81
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
Toward temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. II. Molecular dynamics study of pairs of different types of interactions in water at various temperatures. J Phys Chem B (2012) 0.79
Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions. J Chem Theory Comput (2015) 0.78
Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water. J Phys Chem B (2015) 0.77
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
Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains. J Phys Chem B (2017) 0.75
My 65 years in protein chemistry. Q Rev Biophys (2015) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem (2000) 6.55
Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment. Protein Sci (1993) 1.89
Contribution of unusual arginine-arginine short-range interactions to stabilization and recognition in proteins. J Protein Chem (1994) 1.41
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
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
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
Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc Natl Acad Sci U S A (2005) 2.85
Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc Natl Acad Sci U S A (2002) 2.20
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
Proline cis-trans isomerization and protein folding. Biochemistry (2002) 1.76
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
Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. J Biomol NMR (2006) 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
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
Molecular origin of anticooperativity in hydrophobic association. J Phys Chem B (2005) 1.62
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
Protein-folding dynamics: overview of molecular simulation techniques. Annu Rev Phys Chem (2007) 1.55
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
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
Coarse-grained force field: general folding theory. Phys Chem Chem Phys (2011) 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
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