Published in J Phys Chem B on April 28, 2005
Water in cavity-ligand recognition. J Am Chem Soc (2010) 1.63
Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water. Proc Natl Acad Sci U S A (2007) 1.49
Hydrophobic interactions in model enclosures from small to large length scales: non-additivity in explicit and implicit solvent models. Faraday Discuss (2010) 0.93
Potential of mean force of association of large hydrophobic particles: toward the nanoscale limit. J Phys Chem B (2010) 0.92
Comment on "Molecular origin of anticooperativity in hydrophobic association". J Phys Chem B (2005) 0.79
Liquid-liquid phase separation of N-isopropylpropionamide aqueous solutions above the lower critical solution temperature. Sci Rep (2016) 0.75
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
Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science (2007) 2.24
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
Comparative structural modeling and inference of conserved protein classes in Drosophila seminal fluid. Proc Natl Acad Sci U S A (2004) 1.66
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
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
Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications. J Biol Chem (2003) 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
Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand. Proc Natl Acad Sci U S A (2003) 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
Helix-coil transitions re-visited. Biophys Chem (2002) 1.21
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
Structure of the glucanase inhibitor protein (GIP) family from phytophthora species suggests coevolution with plant endo-beta-1,3-glucanases. Mol Plant Microbe Interact (2008) 1.12
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
Arabidopsis thaliana deficient in two chloroplast ascorbate peroxidases shows accelerated light-induced necrosis when levels of cellular ascorbate are low. Plant Mol Biol (2007) 1.06
How main-chains of proteins explore the free-energy landscape in native states. Proc Natl Acad Sci U S A (2008) 1.06
Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field. J Mol Biol (2010) 1.04
Use of 13Calpha chemical shifts in protein structure determination. J Phys Chem B (2007) 1.04
Module evolution and substrate specificity of fungal nonribosomal peptide synthetases involved in siderophore biosynthesis. BMC Evol Biol (2008) 1.02
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
Structural modules for receptor dimerization in the S-locus receptor kinase extracellular domain. Proc Natl Acad Sci U S A (2007) 1.01
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
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
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