Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials
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Leonidas J. Guibas | Afra Zomorodian | Patrice Koehl | P. Koehl | L. Guibas | A. Zomorodian | L. Guibas
[1] Christopher M. Summa,et al. An atomic environment potential for use in protein structure prediction. , 2005, Journal of molecular biology.
[2] M. Levitt,et al. Improved protein structure selection using decoy-dependent discriminatory functions , 2004, BMC Structural Biology.
[3] Yang Zhang,et al. SPICKER: A clustering approach to identify near‐native protein folds , 2004, J. Comput. Chem..
[4] Hongyi Zhou,et al. Quantifying the effect of burial of amino acid residues on protein stability , 2003, Proteins.
[5] Richard Bonneau,et al. An improved protein decoy set for testing energy functions for protein structure prediction , 2003, Proteins.
[6] M. Levitt,et al. A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. , 2003, Journal of molecular biology.
[7] B. McConkey,et al. Discrimination of native protein structures using atom–atom contact scoring , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[8] Hongyi Zhou,et al. Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction , 2002, Protein science : a publication of the Protein Society.
[9] A. Sali,et al. Statistical potentials for fold assessment , 2009 .
[10] M. Levitt,et al. Extracting knowledge-based energy functions from protein structures by error rate minimization: Comparison of methods using lattice model , 2000 .
[11] M. Karplus,et al. Effective energy functions for protein structure prediction. , 2000, Current opinion in structural biology.
[12] R. Jernigan,et al. An empirical energy potential with a reference state for protein fold and sequence recognition , 1999, Proteins.
[13] M. Hao,et al. Designing potential energy functions for protein folding. , 1999, Current opinion in structural biology.
[14] D. Baker,et al. Clustering of low-energy conformations near the native structures of small proteins. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[15] P. Koehl,et al. Influence of protein structure databases on the predictive power of statistical pair potentials , 1998, Proteins.
[16] F. Melo,et al. Assessing protein structures with a non-local atomic interaction energy. , 1998, Journal of molecular biology.
[17] P. Wolynes,et al. Self-consistently optimized energy functions for protein structure prediction by molecular dynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[18] R. Samudrala,et al. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. , 1998, Journal of molecular biology.
[19] A. Ben-Naim. STATISTICAL POTENTIALS EXTRACTED FROM PROTEIN STRUCTURES : ARE THESE MEANINGFUL POTENTIALS? , 1997 .
[20] A. Finkelstein,et al. Residue-residue mean-force potentials for protein structure recognition. , 1997, Protein engineering.
[21] J Moult,et al. Comparison of database potentials and molecular mechanics force fields. , 1997, Current opinion in structural biology.
[22] F. Melo,et al. Novel knowledge-based mean force potential at atomic level. , 1997, Journal of molecular biology.
[23] F. Eisenhaber. Hydrophobic regions on protein surfaces. Derivation of the solvation energy from their area distribution in crystallographic protein structures , 1996, Protein science : a publication of the Protein Society.
[24] L A Mirny,et al. How to derive a protein folding potential? A new approach to an old problem. , 1996, Journal of molecular biology.
[25] M. Levitt,et al. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. , 1996, Journal of molecular biology.
[26] R. Jernigan,et al. Structure-derived potentials and protein simulations. , 1996, Current opinion in structural biology.
[27] K. Dill,et al. Statistical potentials extracted from protein structures: how accurate are they? , 1996, Journal of molecular biology.
[28] R. Jernigan,et al. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. , 1996, Journal of molecular biology.
[29] P. Koehl,et al. Atomic environment energies in proteins defined from statistics of accessible and contact surface areas. , 1995, Journal of molecular biology.
[30] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[31] M J Sippl,et al. Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.
[32] T. Halgren. Potential energy functions. , 1995, Current opinion in structural biology.
[33] P. Koehl,et al. Polar and nonpolar atomic environments in the protein core: Implications for folding and binding , 1994, Proteins.
[34] E. Shakhnovich,et al. Pseudodihedrals: Simplified protein backbone representation with knowledge‐based energy , 1994, Protein science : a publication of the Protein Society.
[35] S. Wodak,et al. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. , 1994, Journal of molecular biology.
[36] Herbert Edelsbrunner,et al. The union of balls and its dual shape , 1993, SCG '93.
[37] 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 .
[38] Herbert Edelsbrunner,et al. Three-dimensional alpha shapes , 1992, VVS.
[39] G. Crippen,et al. Contact potential that recognizes the correct folding of globular proteins. , 1992, Journal of molecular biology.
[40] D. T. Jones,et al. A new approach to protein fold recognition , 1992, Nature.
[41] M. Sippl,et al. Detection of native‐like models for amino acid sequences of unknown three‐dimensional structure in a data base of known protein conformations , 1992, Proteins.
[42] S. Bryant,et al. The frequency of ion‐pair substructures in proteins is quantitatively related to electrostatic potential: A statistical model for nonbonded interactions , 1991, Proteins.
[43] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[44] M. Sippl. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.
[45] M. Sippl. Calculation of conformational ensembles from potentials of mena force , 1990 .
[46] G. Kolata. High-carb diets questioned. , 1987, Science.
[47] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[48] H. Scheraga,et al. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. , 1976, Macromolecules.
[49] D. Phillips,et al. A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme. , 1969, Journal of molecular biology.
[50] Patrice Koehl,et al. ASTRAL compendium enhancements , 2002, Nucleic Acids Res..
[51] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[52] R Samudrala,et al. Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction , 2000, Protein science : a publication of the Protein Society.
[53] Mark de Berg,et al. Computational geometry: algorithms and applications , 1997 .
[54] Iosif I. Vaisman,et al. Delaunay Tessellation of Proteins: Four Body Nearest-Neighbor Propensities of Amino Acid Residues , 1996, J. Comput. Biol..
[55] D. Eisenberg,et al. A method to identify protein sequences that fold into a known three-dimensional structure. , 1991, Science.
[56] T. Creighton. Proteins: Structures and molecular principles , 1983 .