Published in J Comput Chem on January 15, 2002
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
A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments. J Phys Chem A (2009) 1.39
My 65 years in protein chemistry. Q Rev Biophys (2015) 0.75
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins (2009) 4.27
LRRK2 in Parkinson's disease: protein domains and functional insights. Trends Neurosci (2006) 3.58
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins (2003) 2.77
Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science (2007) 2.24
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
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
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
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
Structural studies of a bacterial condensin complex reveal ATP-dependent disruption of intersubunit interactions. Cell (2009) 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
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
Assessment of predictions submitted for the CASP7 domain prediction category. Proteins (2007) 1.39
Enriching the sequence substitution matrix by structural information. Proteins (2004) 1.36
High accuracy template based modeling by global optimization. Proteins (2007) 1.31
Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test. Acta Crystallogr B (2009) 1.29
PPRODO: prediction of protein domain boundaries using neural networks. Proteins (2005) 1.29
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
An approximately 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. Genome Res (2006) 1.25
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
Unfolded-state dynamics and structure of protein L characterized by simulation and experiment. J Am Chem Soc (2010) 1.18
Structure optimization by conformational space annealing in an off-lattice protein model. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.16
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
All-atom chain-building by optimizing MODELLER energy function using conformational space annealing. Proteins (2009) 1.14
Dynamic similarity of the unfolded states of proteins L and G. Biochemistry (2007) 1.13
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
Protein structure prediction in 2002. Curr Opin Struct Biol (2002) 1.11
Topology of Type II REases revisited; structural classes and the common conserved core. Nucleic Acids Res (2007) 1.11
Polyproline II helix conformation in a proline-rich environment: a theoretical study. Biophys J (2004) 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
Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. PLoS Comput Biol (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
Unbiased global optimization of Lennard-Jones clusters for N < or =201 using the conformational space annealing method. Phys Rev Lett (2003) 1.05
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
Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing. Proteins (2004) 1.03
Module evolution and substrate specificity of fungal nonribosomal peptide synthetases involved in siderophore biosynthesis. BMC Evol Biol (2008) 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
Multiple sequence alignment by conformational space annealing. Biophys J (2008) 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
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
Ruggedness in the folding landscape of protein L. HFSP J (2008) 0.99
The AidB component of the Escherichia coli adaptive response to alkylating agents is a flavin-containing, DNA-binding protein. J Bacteriol (2006) 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
Lignin peroxidase oxidation of veratryl alcohol: effects of the mutants H82A, Q222A, W171A, and F267L. Biochemistry (2002) 0.98
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
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
A tomato endo-beta-1,4-glucanase, SlCel9C1, represents a distinct subclass with a new family of carbohydrate binding modules (CBM49). J Biol Chem (2007) 0.98
Tracing the origin of the fungal α1 domain places its ancestor in the HMG-box superfamily: implication for fungal mating-type evolution. PLoS One (2010) 0.98
Functional dissection of naturally occurring amino acid substitutions in eIF4E that confers recessive potyvirus resistance in plants. Plant Cell (2007) 0.97
Protein-binding site prediction based on three-dimensional protein modeling. Proteins (2009) 0.97
Dissimilarity in the reductive unfolding pathways of two ribonuclease homologues. J Mol Biol (2004) 0.96
Protein structure prediction based on fragment assembly and parameter optimization. Biophys Chem (2005) 0.96
Relation between free energy landscapes of proteins and dynamics. J Chem Theory Comput (2010) 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
Refinement of protein termini in template-based modeling using conformational space annealing. Proteins (2011) 0.95
A surface loop of the potato leafroll virus coat protein is involved in virion assembly, systemic movement, and aphid transmission. J Virol (2005) 0.94
Sann: solvent accessibility prediction of proteins by nearest neighbor method. Proteins (2012) 0.93
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
Building and assessing atomic models of proteins from structural templates: learning and benchmarks. Proteins (2009) 0.92
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