Published in Protein Sci on October 01, 1993
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
Protein structure prediction by global optimization of a potential energy function. Proc Natl Acad Sci U S A (1999) 2.66
Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. Proc Natl Acad Sci U S A (1999) 1.99
Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment. Protein Sci (1993) 1.89
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
Principal component analysis for protein folding dynamics. J Mol Biol (2008) 1.42
Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field. J Chem Theory Comput (2006) 1.27
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A (2010) 1.19
Free energies of protein decoys provide insight into determinants of protein stability. Protein Sci (2001) 1.04
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
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
A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins. 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
Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix. Phys Rev Lett (2013) 0.88
The Role of Aromatic Residues in Stabilizing the Secondary and Tertiary Structure of Avian Pancreatic Polypeptide. Int J Quantum Chem (2008) 0.88
Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain. J Mol Biol (2012) 0.86
Local vs global motions in protein folding. J Chem Theory Comput (2013) 0.84
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
Hidden protein folding pathways in free-energy landscapes uncovered by network analysis. J Chem Theory Comput (2012) 0.83
UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. Bioinformatics (2016) 0.82
Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues. J Chem Theory Comput (2012) 0.82
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
Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field. J Chem Theory Comput (2008) 0.80
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
Bioinformatics and computational biology in Poland. PLoS Comput Biol (2013) 0.77
DNA Duplex Formation with a Coarse-Grained Model. J Chem Theory Comput (2014) 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
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinformatics (2016) 0.75
Some factors in the interpretation of protein denaturation. Adv Protein Chem (1959) 24.89
Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng (1977) 16.38
A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol (1976) 7.06
Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci U S A (1987) 5.84
Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules (1977) 3.53
Origins of structure in globular proteins. Proc Natl Acad Sci U S A (1990) 3.09
Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. Macromolecules (1977) 2.59
Conformations of folded proteins in restricted spaces. Biochemistry (1990) 2.48
Theory for protein mutability and biogenesis. Proc Natl Acad Sci U S A (1990) 2.31
Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor. Proteins (1991) 1.65
On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method--tests on poly(L-alanine). Biopolymers (1988) 1.62
Low-energy structures of two dipeptides and their relationship to bend conformations. Macromolecules (1975) 1.45
Quantitative organization of the known protein x-ray structures. I. Methods and short-length-scale results. Proteins (1990) 1.37
Conformational flexibility in a small globular hormone: x-ray analysis of avian pancreatic polypeptide at 0.98-A resolution. Biopolymers (1983) 1.33
Influence of water on protein structure. An analysis of the preferences of amino acid residues for the inside or outside and for specific conformations in a protein molecule. Macromolecules (1978) 1.29
On the multiple-minima problem in the conformational analysis of polypeptides. I. Backbone degrees of freedom for a perturbed alpha-helix. Biopolymers (1987) 1.22
A 1.8 A resolution potential function for protein folding. Biopolymers (1990) 0.99
The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: tests on enkephalin. J Protein Chem (1989) 0.97
Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor. Proteins (1992) 0.95
Conformation and association of pancreatic polypeptide from three species. Biochemistry (1980) 0.92
Sidechain and backbone potential function for conformational analysis of proteins. Int J Pept Protein Res (1985) 0.92
Reversible dimerization of avian pancreatic polypeptide. Biochemistry (1980) 0.90
Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins. Proc Natl Acad Sci U S A (1977) 0.89
Molecular mechanics calculations on deaminooxytocin and on deamino-arginine-vasopressin and its analogues. J Comput Aided Mol Des (1989) 0.80
Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci U S A (1987) 5.84
Regulation of JNK signaling by GSTp. EMBO J (1999) 4.06
Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci U S A (1987) 3.68
Conformation of analysis of macromolecules. IV. Helical structures of poly-L-alanine, poly-L-valine, poly-beta-methyl-L-aspartate, poly-gamma-methyl-L-glutamate, and poly-L-tyrosine. J Chem Phys (1967) 3.61
Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules (1977) 3.53
Experimental and theoretical aspects of protein folding. Adv Protein Chem (1975) 3.51
Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptide. Proc Natl Acad Sci U S A (1967) 3.26
Chain reversals in proteins. Biochim Biophys Acta (1973) 3.18
Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proc Natl Acad Sci U S A (1971) 2.68
Protein structure prediction by global optimization of a potential energy function. Proc Natl Acad Sci U S A (1999) 2.66
Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. Macromolecules (1977) 2.59
Assessment of some problems associated with prediction of the three-dimensional structure of a protein from its amino-acid sequence. Proc Natl Acad Sci U S A (1975) 2.49
Global optimization of clusters, crystals, and biomolecules. Science (1999) 2.33
Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc Natl Acad Sci U S A (2001) 2.31
MEKK1/JNK signaling stabilizes and activates p53. Proc Natl Acad Sci U S A (1998) 2.27
Computation of the sterically allowed conformations of peptides. Biopolymers (1966) 2.27
Protein folding. Q Rev Biophys (1977) 2.21
Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin. Biopolymers (1985) 2.18
Status of empirical methods for the prediction of protein backbone topography. Biochemistry (1976) 2.12
The effect of neighboring charges on the helix forming ability of charged amino acids in proteins. Macromolecules (1976) 2.08
A proposal of standard conventions and nomenclature for the description of polypeptide conformations. J Mol Biol (1966) 2.05
Disulfide bonds and protein folding. Biochemistry (2000) 2.03
Conformational studies of poly-L-alanine in water. Biopolymers (1968) 2.02
Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. Proc Natl Acad Sci U S A (1999) 1.99
Influence of flexibility on the energy contours of dipeptide maps. Biopolymers (1966) 1.93
The influence of long-range interactions on the structure of myoglobin. Biochemistry (1968) 1.91
Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment. Protein Sci (1993) 1.89
Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc Natl Acad Sci U S A (2000) 1.88
Assignment of the histidine peaks in the nuclear magnetic resonance spectrum of ribonuclease. Proc Natl Acad Sci U S A (1968) 1.83
Helix probability profiles of denatured proteins and their correlation with native structures. Proc Natl Acad Sci U S A (1970) 1.81
A second right-handed helical structure with the parameters of the Pauling-Corey alpha-helix. Nature (1967) 1.81
Minimization of polypeptide energy. II. Preliminary structures of oxytocin, vasopressin, and an octapeptide from ribonuclease. Proc Natl Acad Sci U S A (1967) 1.80
Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor. Proteins (1991) 1.65
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 proposal of standard conventions and nomenclature for the description of polypeptide conformation. J Biol Chem (1966) 1.65
On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method--tests on poly(L-alanine). Biopolymers (1988) 1.62
Recent progress in the theoretical treatment of protein folding. Biopolymers (1983) 1.58
Jun NH2-terminal kinase phosphorylation of p53 on Thr-81 is important for p53 stabilization and transcriptional activities in response to stress. Mol Cell Biol (2001) 1.54
An electron microscopic investigation of the polymerization of bovine fibrin monomer. J Mol Biol (1972) 1.52
Conformation-dependent phosphorylation of p53. Proc Natl Acad Sci U S A (1997) 1.49
Cooperative interactions in single-strand oligomers of adenylic acid. Biopolymers (1966) 1.48
Role of medium-range interactions in proteins. Proc Natl Acad Sci U S A (1973) 1.47
Proline-induced constraints in alpha-helices. Biopolymers (1987) 1.47
Influence of local interactions on protein structure. I. Conformational energy studies of N-acetyl-N'-methylamides of Pro-X and X-Pro dipeptides. Biopolymers (1977) 1.46
Low-energy structures of two dipeptides and their relationship to bend conformations. Macromolecules (1975) 1.45
Energetics of the structure of the four-alpha-helix bundle in proteins. Proc Natl Acad Sci U S A (1988) 1.44
Use of buildup and energy-minimization procedures to compute low-energy structures of the backbone of enkephalin. Biopolymers (1985) 1.43
Intramolecular forces and protein conformation. Discuss Faraday Soc (1965) 1.43
Use of a symmetry condition to compute the conformation of gramicidin S1. Macromolecules (1976) 1.41
Kinetics of competitive binding with application to thrombin complexes. Anal Biochem (1997) 1.41
Contribution of unusual arginine-arginine short-range interactions to stabilization and recognition in proteins. J Protein Chem (1994) 1.41
The influence of short-range interactions on protein conformation. I. Side chain-backbone interactions within a single peptide unit. Proc Natl Acad Sci U S A (1968) 1.41
Computation of structures of homologous proteins. Alpha-lactalbumin from lysozyme. Biochemistry (1974) 1.41
Initial attempts at a theoretical calculation of the conformation of gramicidin-S. Biochemistry (1966) 1.40
Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides. J Mol Biol (1996) 1.40
Calculation of protein conformation by global optimization of a potential energy function. Proteins (1999) 1.37
Prediction of the three-dimensional structure of the transforming region of the EJ/T24 human bladder oncogene product and its normal cellular homologue. Proc Natl Acad Sci U S A (1983) 1.37
Calculation of the three-dimensional structure of the membrane-bound portion of melittin from its amino acid sequence. Proc Natl Acad Sci U S A (1982) 1.37
A third blind test of crystal structure prediction. Acta Crystallogr B (2005) 1.36
Optimized representations and maximal information in proteins. Proteins (2000) 1.35
Theoretical and experimental studies of conformations of polypeptides. Chem Rev (1971) 1.35
The effect of D2-O on the thermal stability of proteins. Thermodynamic parameters for the transfer of model compounds from H2-O to D2-O. J Phys Chem (1965) 1.34
Solution of the embedding problem and decomposition of symmetric matrices. Proc Natl Acad Sci U S A (1985) 1.34
Predictions of structural homologies in cytochrome c proteins. Arch Biochem Biophys (1971) 1.32
Characterization of multiple bends in proteins. Biopolymers (1980) 1.32
Nuclear magnetic resonance spectrum of lysine-vasopressin and its structural implications. Proc Natl Acad Sci U S A (1971) 1.31
Local interactions in bends of proteins. Proc Natl Acad Sci U S A (1977) 1.30
Influence of water on protein structure. An analysis of the preferences of amino acid residues for the inside or outside and for specific conformations in a protein molecule. Macromolecules (1978) 1.29
Oxidative folding of proteins. Acc Chem Res (2000) 1.27
Conformational and molecular basis for induction of apoptosis by a p53 C-terminal peptide in human cancer cells. J Biol Chem (1999) 1.27
The intrinsic helix-forming tendency of L-alanine. Proc Natl Acad Sci U S A (1992) 1.26
Sensitive quantitative analysis of disulfide bonds in polypeptides and proteins. Anal Biochem (1984) 1.26
Solution structure of murine epidermal growth factor: determination of the polypeptide backbone chain-fold by nuclear magnetic resonance and distance geometry. Proc Natl Acad Sci U S A (1987) 1.24
Structure of the interferon-receptor complex determined by distance constraints from double-mutant cycles and flexible docking. Proc Natl Acad Sci U S A (2001) 1.23
Prediction of the three-dimensional structure of the leader sequence of pre-kappa light chain, a hexadecapeptide. Proc Natl Acad Sci U S A (1982) 1.22
Energy parameters in polypeptides. V. An empirical hydrogen bond potential function based on molecular orbital calculations. J Phys Chem (1972) 1.22
On the multiple-minima problem in the conformational analysis of polypeptides. I. Backbone degrees of freedom for a perturbed alpha-helix. Biopolymers (1987) 1.22
Designing potential energy functions for protein folding. Curr Opin Struct Biol (1999) 1.21
Disulfide bond dihedral angles from Raman spectroscopy. Proc Natl Acad Sci U S A (1973) 1.20
Stability of polypeptide conformational states as determined by computer simulation of the free energy. Biopolymers (1987) 1.20
Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein. Biochemistry (2001) 1.20
Molecular simulation study of cooperativity in hydrophobic association. Protein Sci (2000) 1.18
Conformational energy studies of beta-sheets of model silk fibroin peptides. I. Sheets of poly(Ala-Gly) chains. Biopolymers (1991) 1.18
The influence of short-range interactions on protein onformation. II. A model for predicting the alpha-helical regions of proteins. Proc Natl Acad Sci U S A (1969) 1.18
Conformational energy calculations on polypeptides and proteins: use of a statistical mechanical procedure for evaluating structure and properties. Ann N Y Acad Sci (1986) 1.17
Statistical and energetic analysis of side-chain conformations in oligopeptides. Int J Pept Protein Res (1983) 1.17
Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. III. Probable and average conformations of enkephalin. Biopolymers (1987) 1.17
How optimization of potential functions affects protein folding. Proc Natl Acad Sci U S A (1996) 1.16
Phase transitions in one dimension and the helix-coil transition in polyamino acids. J Chem Phys (1966) 1.16
Enkephalin: conformational analysis by means of empirical energy calculations. Proc Natl Acad Sci U S A (1977) 1.16
Model of protein folding: inclusion of short-, medium-, and long-range interactions. Proc Natl Acad Sci U S A (1975) 1.16
Influence of an extrinsic cross-link on the folding pathway of ribonuclease A. Conformational and thermodynamic analysis of cross-linked (lysine7-lysine41)-ribonuclease a. Biochemistry (1984) 1.16