Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
暂无分享,去创建一个
[1] R. Kubo. GENERALIZED CUMULANT EXPANSION METHOD , 1962 .
[2] D. Marquardt. An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .
[3] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[4] P K Warme,et al. Computation of structures of homologous proteins. Alpha-lactalbumin from lysozyme. , 1974, Biochemistry.
[5] H A Scheraga,et al. Low-energy structures of two dipeptides and their relationship to bend conformations. , 1974, Macromolecules.
[6] M. Levitt,et al. Computer simulation of protein folding , 1975, Nature.
[7] M. Levitt. A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.
[8] H. Scheraga,et al. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. , 1976, Macromolecules.
[9] H. Scheraga,et al. Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. , 1977, Macromolecules.
[10] G J Williams,et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.
[11] Harold A. Scheraga,et al. An approximate treatment of long-range interactions in proteins , 1977 .
[12] B. Berne. Modification of the overlap potential to mimic a linear site-site potential , 1981 .
[13] A potential function for conformational analysis of proteins. , 2009, International journal of peptide and protein research.
[14] E. Baker,et al. Hydrogen bonding in globular proteins. , 1984, Progress in biophysics and molecular biology.
[15] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[16] T. A. Jones,et al. Using known substructures in protein model building and crystallography. , 1986, The EMBO journal.
[17] H A Scheraga,et al. On the multiple‐minima problem in the conformational analysis of polypeptides. I. Backbone degrees of freedom for a perturbed α‐helix , 1987 .
[18] F E Cohen,et al. Novel method for the rapid evaluation of packing in protein structures. , 1990, Journal of molecular biology.
[19] D A Clark,et al. Protein topology prediction through constraint-based search and the evaluation of topological folding rules. , 1991, Protein engineering.
[20] Paul R. Gerber,et al. Peptide mechanics: A force field for peptides and proteins working with entire residues as smallest units , 1992 .
[21] G. Crippen,et al. Contact potential that recognizes the correct folding of globular proteins. , 1992, Journal of molecular biology.
[22] M J Rooman,et al. Extracting information on folding from the amino acid sequence: consensus regions with preferred conformation in homologous proteins. , 1992, Biochemistry.
[23] P. Wolynes,et al. Protein tertiary structure recognition using optimized Hamiltonians with local interactions. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[24] John P. Overington,et al. Alignment and searching for common protein folds using a data bank of structural templates. , 1993, Journal of molecular biology.
[25] S. Rackovsky,et al. Prediction of protein conformation on the basis of a search for compact structures: Test on avian pancreatic polypeptide , 1993, Protein science : a publication of the Protein Society.
[26] S. Rackovsky,et al. Calculation of protein backbone geometry from α‐carbon coordinates based on peptide‐group dipole alignment , 1993, Protein science : a publication of the Protein Society.
[27] Adam Godzik,et al. De novo and inverse folding predictions of protein structure and dynamics , 1993, J. Comput. Aided Mol. Des..
[28] A. Godzik,et al. A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins , 1993 .
[29] Manfred J. Sippl,et al. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures , 1993, J. Comput. Aided Mol. Des..
[30] J. Skolnick,et al. Monte carlo simulations of protein folding. I. Lattice model and interaction scheme , 1994, Proteins.
[31] H. Scheraga,et al. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides , 1994 .
[32] J. Skolnick,et al. Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin , 1994, Proteins.
[33] M. Hao,et al. STATISTICAL THERMODYNAMICS OF PROTEIN FOLDING : SEQUENCE DEPENDENCE , 1994 .
[34] Darren Redfern,et al. The Maple handbook , 1994 .
[35] A. Wallqvist,et al. A simplified amino acid potential for use in structure predictions of proteins , 1994, Proteins.
[36] Adam Liwo,et al. Comparison of the low energy conformations of an oncogenic and a non-oncogenic p21 protein, neither of which binds GTP or GDP , 1994, Journal of protein chemistry.
[37] E. Shakhnovich,et al. Pseudodihedrals: Simplified protein backbone representation with knowledge‐based energy , 1994, Protein science : a publication of the Protein Society.
[38] H A Scheraga,et al. Recent developments in the theory of protein folding: searching for the global energy minimum. , 1996, Biophysical chemistry.
[39] M. Hao,et al. How optimization of potential functions affects protein folding. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[40] D Fischer,et al. Assigning amino acid sequences to 3‐dimensional protein folds , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[41] G M Crippen. Easily searched protein folding potentials. , 1996, Journal of molecular biology.
[42] J. Skolnick,et al. MONSSTER: a method for folding globular proteins with a small number of distance restraints. , 1997, Journal of molecular biology.
[43] A. Liwo,et al. A united‐residue force field for off‐lattice protein‐structure simulations. I. Functional forms and parameters of long‐range side‐chain interaction potentials from protein crystal data , 1997 .
[44] New optimization method for conformational energy calculations on polypeptides: Conformational space annealing , 1997 .
[45] A. Liwo,et al. A united‐residue force field for off‐lattice protein‐structure simulations. II. Parameterization of short‐range interactions and determination of weights of energy terms by Z‐score optimization , 1997 .
[46] D. Baker,et al. Prediction of local structure in proteins using a library of sequence-structure motifs. , 1998, Journal of molecular biology.
[47] Tanja Kortemme,et al. Design of a 20-Amino Acid, Three-Stranded β-Sheet Protein , 1998 .
[48] D. Thirumalai,et al. LINKING RATES OF FOLDING IN LATTICE MODELS OF PROTEINS WITH UNDERLYING THERMODYNAMIC CHARACTERISTICS , 1998, cond-mat/9805061.
[49] A. Liwo,et al. United‐residue force field for off‐lattice protein‐structure simulations: III. Origin of backbone hydrogen‐bonding cooperativity in united‐residue potentials , 1998 .
[50] S. Rackovsky,et al. Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. , 1998, Biopolymers.
[51] P. Derreumaux. From polypeptide sequences to structures using Monte Carlo simulations and an optimized potential , 1999 .
[52] A. Liwo,et al. Protein structure prediction by global optimization of a potential energy function. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[53] Harold A. Scheraga,et al. Conformational space annealing by parallel computations: Extensive conformational search of Met‐enkephalin and of the 20‐residue membrane‐bound portion of melittin , 1999 .
[54] Adam Liwo,et al. Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods , 1999 .
[55] A. Liwo,et al. 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. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[56] Adam Liwo,et al. Surmounting the Multiple-Minima Problem in Protein Folding , 1999, J. Glob. Optim..
[57] H A Scheraga,et al. Molecular simulation study of cooperativity in hydrophobic association , 2000, Protein science : a publication of the Protein Society.
[58] Adam Liwo,et al. Recent improvements in prediction of protein structure by global optimization of a potential energy function , 2001, Proceedings of the National Academy of Sciences of the United States of America.