PubRank

Harold A Scheraga

Author PubWeight™ 157.86‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 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
2 Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc Natl Acad Sci U S A 2002 2.20
3 Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins. J Phys Chem B 2007 2.19
4 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
5 Proline cis-trans isomerization and protein folding. Biochemistry 2002 1.76
6 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
7 Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. J Biomol NMR 2006 1.71
8 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
9 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
10 Molecular origin of anticooperativity in hydrophobic association. J Phys Chem B 2005 1.62
11 Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation. Proc Natl Acad Sci U S A 2009 1.59
12 Predicting 13Calpha chemical shifts for validation of protein structures. J Biomol NMR 2007 1.59
13 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
14 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
15 Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol 2008 1.54
16 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
17 The role of hydrophobic interactions in initiation and propagation of protein folding. Proc Natl Acad Sci U S A 2006 1.42
18 Principal component analysis for protein folding dynamics. J Mol Biol 2008 1.42
19 Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test. Acta Crystallogr B 2011 1.40
20 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
21 Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test. Acta Crystallogr B 2009 1.29
22 Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry. Biochemistry 2006 1.28
23 Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field. J Chem Theory Comput 2006 1.27
24 Addition of side chains to a known backbone with defined side-chain centroids. Biophys Chem 2003 1.27
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
26 Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains. J Phys Chem B 2007 1.24
27 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
28 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
29 Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A 2010 1.19
30 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
31 Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model. J Phys Chem B 2007 1.15
32 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
33 Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method. J Comput Chem 2002 1.15
34 Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures. Proteins 2008 1.14
35 Sequential nearest-neighbor effects on computed 13Calpha chemical shifts. J Biomol NMR 2010 1.14
36 Topology of Type II REases revisited; structural classes and the common conserved core. Nucleic Acids Res 2007 1.11
37 Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts. Acc Chem Res 2009 1.11
38 Polyproline II helix conformation in a proline-rich environment: a theoretical study. Biophys J 2004 1.10
39 A new force field (ECEPP-05) for peptides, proteins, and organic molecules. J Phys Chem B 2006 1.10
40 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
41 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
42 beta-hairpin-forming peptides; models of early stages of protein folding. Biophys Chem 2010 1.07
43 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
44 How main-chains of proteins explore the free-energy landscape in native states. Proc Natl Acad Sci U S A 2008 1.06
45 Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field. J Mol Biol 2010 1.04
46 Use of 13Calpha chemical shifts in protein structure determination. J Phys Chem B 2007 1.04
47 Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field. J Comput Chem 2010 1.03
48 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
49 Packing helices in proteins by global optimization of a potential energy function. Proc Natl Acad Sci U S A 2003 1.00
50 Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: a theoretical study. J Biomol NMR 2002 1.00
51 Further evidence for the absence of polyproline II stretch in the XAO peptide. Biophys J 2007 1.00
52 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
53 Performance of density functional models to reproduce observed (13)C(alpha) chemical shifts of proteins in solution. J Comput Chem 2009 0.99
54 Coarse-grained force field: general folding theory. Phys Chem Chem Phys 2011 0.99
55 Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles. Biophys Chem 2003 0.99
56 Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method. J Comput Chem 2010 0.99
57 How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics? Phys Rev Lett 2009 0.99
58 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
59 What can we learn by computing 13Calpha chemical shifts for X-ray protein models? Acta Crystallogr D Biol Crystallogr 2009 0.98
60 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
61 Dissimilarity in the reductive unfolding pathways of two ribonuclease homologues. J Mol Biol 2004 0.96
62 Relation between free energy landscapes of proteins and dynamics. J Chem Theory Comput 2010 0.96
63 On the orientation of the backbone dipoles in native folds. Proc Natl Acad Sci U S A 2005 0.96
64 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
65 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
66 Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy. J Phys Chem B 2007 0.94
67 Potential of mean force of hydrophobic association: dependence on solute size. J Phys Chem B 2007 0.93
68 Intramolecular versus intermolecular disulfide bonds in prion proteins. J Biol Chem 2002 0.92
69 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
70 Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins. J Phys Chem B 2007 0.92
71 Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure. Proteins 2009 0.92
72 Potential of mean force of association of large hydrophobic particles: toward the nanoscale limit. J Phys Chem B 2010 0.92
73 PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. J Mol Biol 2010 0.91
74 Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. J Chem Theory Comput 2012 0.91
75 Influence of charge and size of terminal amino-acid residues on local conformational states and shape of alanine-based peptides. Biopolymers 2008 0.91
76 Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin. Biochemistry 2004 0.90
77 Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation. Proteins 2009 0.90
78 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
79 Characterization of the fast-forming intermediate, des [30-75], in the reductive unfolding of onconase. Biochemistry 2004 0.89
80 Unblocked statistical-coil tetrapeptides in aqueous solution: quantum-chemical computation of the carbon-13 NMR chemical shifts. J Biomol NMR 2003 0.89
81 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
82 Inhibitor design by wrapping packing defects in HIV-1 proteins. Proc Natl Acad Sci U S A 2004 0.89
83 FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins. J Phys Chem B 2008 0.89
84 Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. Phys Rev Lett 2013 0.88
85 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
86 WeFold: a coopetition for protein structure prediction. Proteins 2014 0.88
87 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
88 Coarse-grained model of nucleic acid bases. J Comput Chem 2010 0.86
89 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
90 CheShift-2: graphic validation of protein structures. Bioinformatics 2012 0.86
91 Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain. J Mol Biol 2012 0.86
92 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
93 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
94 A new method for rapid characterization of the folding pathways of multidisulfide-containing proteins. J Am Chem Soc 2004 0.86
95 Analysis of 13Calpha and 13Cbeta chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach. J Biomol NMR 2010 0.85
96 Simultaneous characterization of the reductive unfolding pathways of RNase B isoforms by top-down mass spectrometry. Chem Biol 2004 0.85
97 Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between theory and experiment. Biopolymers 2008 0.85
98 Assessment of two theoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment. J Phys Chem B 2006 0.85
99 Coupling between conformation and proton binding in proteins. Proteins 2005 0.85
100 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
101 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
102 Oxidative folding and N-terminal cyclization of onconase. Biochemistry 2007 0.84
103 Dissimilarity in the oxidative folding of onconase and ribonuclease A, two structural homologues. Protein Eng Des Sel 2008 0.84
104 Local vs global motions in protein folding. J Chem Theory Comput 2013 0.84
105 A localized specific interaction alters the unfolding pathways of structural homologues. J Am Chem Soc 2006 0.84
106 Fast and accurate computation of the 13C chemical shifts for an alanine-rich peptide. Proteins 2004 0.84
107 Hidden protein folding pathways in free-energy landscapes uncovered by network analysis. J Chem Theory Comput 2012 0.83
108 Conformational studies of the C-terminal 16-amino-acid-residue fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus. Biopolymers 2009 0.83
109 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
110 Trimethylamine-N-oxide modulates the reductive unfolding of onconase. Biochem Biophys Res Commun 2004 0.82
111 Interplay of charge distribution and conformation in peptides: comparison of theory and experiment. Biopolymers 2005 0.82
112 Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long-range hydrophobic interactions. Proteins 2010 0.82
113 Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC. J Comput Chem 2005 0.82
114 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
115 Oxidative folding pathway of onconase, a ribonuclease homologue: insight into oxidative folding mechanisms from a study of two homologues. Biochemistry 2009 0.81
116 Proline isomerization in bovine pancreatic ribonuclease A. 2. Folding conditions. Biochemistry 2003 0.81
117 Ab initio structure prediction of two alpha-helical oligomers with a multiple-chain united-residue force field and global search. Biopolymers 2003 0.81
118 A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions. J Mol Model 2014 0.81
119 Physics-based method to validate and repair flaws in protein structures. Proc Natl Acad Sci U S A 2013 0.81
120 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
121 Factors affecting the computation of the 13C shielding in disaccharides. J Comput Chem 2014 0.81
122 Use of decoys to optimize an all-atom force field including hydration. Biophys J 2008 0.80
123 Exercises in prognostication: crystal structures and protein folding. Proc Natl Acad Sci U S A 2004 0.80
124 Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field. J Chem Theory Comput 2008 0.80
125 Position dependence of the 13C chemical shifts of alpha-helical model peptides. Fingerprint of the 20 naturally occurring amino acids. Protein Sci 2004 0.79
126 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
127 CheShift-2 resolves a local inconsistency between two X-ray crystal structures. J Biomol NMR 2012 0.78
128 Role of the [65-72] disulfide bond in oxidative folding of bovine pancreatic ribonuclease A. Biochemistry 2003 0.78
129 Coexistence of phases in a protein heterodimer. J Chem Phys 2012 0.78
130 A generalized G-SFED continuum solvation free energy calculation model. Proc Natl Acad Sci U S A 2013 0.78
131 Effect of protein disulfide isomerase on the rate-determining steps of the folding of bovine pancreatic ribonuclease A. FEBS Lett 2002 0.78
132 Challenges in structure prediction of oligomeric proteins at the united-residue level: searching the multiple-chain energy landscape with CSA and CFMC. Biopolymers 2003 0.78
133 High level production of bovine angiogenin in E. coli by an efficient refolding procedure. Biotechnol Lett 2004 0.78
134 A novel method to determine thermal transition curves of disulfide-containing proteins and their structured folding intermediates. Biochem Biophys Res Commun 2003 0.78
135 Conformational studies of the alpha-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus. Biopolymers 2008 0.78
136 Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions. J Chem Theory Comput 2015 0.78
137 Like-charged residues at the ends of oligoalanine sequences might induce a chain reversal. Biopolymers 2011 0.77
138 Common functionally important motions of the nucleotide-binding domain of Hsp70. Proteins 2014 0.77
139 An efficient method for calculating atomic charges of peptides and proteins from electronic populations. J Phys Chem B 2008 0.77
140 Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone. J Chem Phys 2007 0.77
141 Assessing the magnitude of folding forces along the oxidative folding pathway of multi-disulfide-containing proteins. J Am Chem Soc 2003 0.77
142 Are accurate computations of the 13C' shielding feasible at the DFT level of theory? J Comput Chem 2013 0.77
143 Implementation of a k/k(0) method to identify long-range structure in transition states during conformational folding/unfolding of proteins. Structure 2007 0.77
144 A united residue force-field for calcium-protein interactions. Protein Sci 2004 0.77
145 New Insights into Protein (Un)Folding Dynamics. J Phys Chem Lett 2015 0.77
146 Detecting native folds in mixtures of proteins that contain disulfide bonds. Nat Biotechnol 2008 0.76
147 Development of a novel method to populate native disulfide-bonded intermediates for structural characterization of proteins: implications for the mechanism of oxidative folding of RNase A. J Am Chem Soc 2002 0.76
148 The oxidative folding rate of bovine pancreatic ribonuclease is enhanced by a covalently attached oligosaccharide. Biochemistry 2005 0.76
149 Correlation of folding kinetics with the number and isomerization states of prolines in three homologous proteins of the RNase family. FEBS Lett 2006 0.76
150 Interactions that favor the native over the non-native disulfide bond among residues 58-72 in the oxidative folding of bovine pancreatic ribonuclease A. Biochemistry 2002 0.76
151 Formation of the hydrophobic core of ribonuclease A through sequential coordinated conformational transitions. Biochemistry 2002 0.76
152 Shifting the competition between the intramolecular Reshuffling reaction and the direct oxidation reaction during the oxidative folding of kinetically trapped disulfide-insecure intermediates. Biochemistry 2003 0.76
153 Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints. Proteins 2008 0.76
154 Native conformational tendencies in unfolded polypeptides: development of a novel method to assess native conformational tendencies in the reduced forms of multiple disulfide-bonded proteins. J Am Chem Soc 2003 0.76
155 Identification of formation of initial native structure in onconase from an unfolded state. Biochemistry 2011 0.75
156 Effects of tyrosine mutations on the conformational and oxidative folding of ribonuclease a: a comparative study. Biochemistry 2009 0.75
157 Influence of the Length of the Alanine Spacer on the Acidic-Basic Properties of the Ac-Lys-(Ala)(n)-Lys-NH(2) Peptides (n = 0, 1, 2, …, 5). J Solution Chem 2012 0.75
158 Role of the surface loop on the structure and biological activity of angiogenin. BMB Rep 2009 0.75
159 Oxidative folding of bovine pancreatic ribonuclease A: insight into the overall catalysis of the refolding pathway by phosphate. J Protein Chem 2002 0.75
160 Characterizing the unstructured intermediates in oxidative folding. Biochemistry 2003 0.75
161 Model for the crystal packing and conformational changes of biphenyl in incommensurate phase transitions. Acta Crystallogr B 2004 0.75