Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
暂无分享,去创建一个
C Kooperberg | D Baker | K T Simons | E Huang | D. Baker | E. Huang | C. Kooperberg | K. Simons | C. Kooperberg | E. Huang | D. Baker | D. Baker
[1] W. Wooster,et al. Crystal structure of , 2005 .
[2] R. Friesner,et al. Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models. , 1995, Journal of molecular biology.
[3] W. Braun,et al. Predicting the helix packing of globular proteins by self‐correcting distance geometry , 1995, Protein science : a publication of the Protein Society.
[4] 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.
[5] Peter E. Hart,et al. Pattern classification and scene analysis , 1974, A Wiley-Interscience publication.
[6] A. Beyer,et al. An improved pair potential to recognize native protein folds , 1994, Proteins.
[7] M Levitt,et al. Recognizing native folds by the arrangement of hydrophobic and polar residues. , 1995, Journal of molecular biology.
[8] 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.
[9] J. Deisenhofer. Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution. , 1981, Biochemistry.
[10] Alfonso Mondragón,et al. STRUCTURE OF PHAGE 434 CRO PROTEIN AT 2.35 ANGSTROMS RESOLUTION , 1989 .
[11] Carl O. Pabo,et al. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 Å resolution: A framework for understanding homeodomain-DNA interactions , 1990, Cell.
[12] A. Gronenborn,et al. A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. , 1993, Science.
[13] 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..
[14] D. Baker,et al. Recurring local sequence motifs in proteins. , 1995, Journal of molecular biology.
[15] A. Elofsson,et al. Local moves: An efficient algorithm for simulation of protein folding , 1995, Proteins.
[16] D Baker,et al. Global properties of the mapping between local amino acid sequence and local structure in proteins. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[17] E S Huang,et al. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. , 1997, Journal of molecular biology.
[18] C. Sander,et al. Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.
[19] J. Thornton,et al. PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .
[20] S Subbiah,et al. Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution. , 1989, Journal of molecular biology.
[21] K. Dill,et al. Statistical potentials extracted from protein structures: how accurate are they? , 1996, Journal of molecular biology.
[22] S. Henikoff,et al. Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[23] J Moult,et al. Genetic algorithms for protein structure prediction. , 1996, Current opinion in structural biology.
[24] J. Moult,et al. Determination of the conformation of folding initiation sites in proteins by computer simulation , 1995, Proteins.
[25] A. Liljas,et al. Structure of the C-terminal domain of the ribosomal protein L7/L12 from Escherichia coli at 1.7 A. , 1987, Journal of molecular biology.
[26] K Yue,et al. Folding proteins with a simple energy function and extensive conformational searching , 1996, Protein science : a publication of the Protein Society.
[27] S. Forsén,et al. Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography. , 1992, Journal of molecular biology.
[28] D. Eisenberg,et al. An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[29] P. Kraulis. A program to produce both detailed and schematic plots of protein structures , 1991 .
[30] M. Sippl. Calculation of conformational ensembles from potentials of mena force , 1990 .
[31] Burkhard Rost,et al. PHD - an automatic mail server for protein secondary structure prediction , 1994, Comput. Appl. Biosci..
[32] G J Williams,et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.
[33] K. Dill,et al. A simple protein folding algorithm using a binary code and secondary structure constraints. , 1995, Protein engineering.
[34] F. Cohen,et al. Multiple sequence information for threading algorithms. , 1996, Journal of molecular biology.
[35] V Muñoz,et al. Local versus nonlocal interactions in protein folding and stability--an experimentalist's point of view. , 1996, Folding & design.
[36] Jorja G. Henikoff,et al. Using substitution probabilities to improve position-specific scoring matrices , 1996, Comput. Appl. Biosci..
[37] S. Harrison,et al. Structure of phage 434 Cro protein at 2.35 A resolution. , 1989, Journal of molecular biology.
[38] E. Lander,et al. Protein secondary structure prediction using nearest-neighbor methods. , 1993, Journal of molecular biology.
[39] R. Huber,et al. Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement , 1991 .
[40] U. Hobohm,et al. Selection of representative protein data sets , 1992, Protein science : a publication of the Protein Society.
[41] S. Wodak,et al. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. , 1994, Journal of molecular biology.
[42] L Serrano,et al. Folding kinetics of Che Y mutants with enhanced native alpha-helix propensities. , 1997, Journal of molecular biology.
[43] P Argos,et al. Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions. , 1996, Journal of molecular biology.
[44] S. Doniach,et al. A computer model to dynamically simulate protein folding: Studies with crambin , 1989, Proteins.
[45] R. Jernigan,et al. Structure-derived potentials and protein simulations. , 1996, Current opinion in structural biology.
[46] D Baker,et al. A desolvation barrier to hydrophobic cluster formation may contribute to the rate‐limiting step in protein folding , 1997, Protein science : a publication of the Protein Society.
[47] M. Sternberg,et al. On the prediction of protein structure: The significance of the root-mean-square deviation. , 1980, Journal of molecular biology.
[48] D. T. Jones,et al. A new approach to protein fold recognition , 1992, Nature.
[49] N. D. Clarke,et al. Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures , 1990, Proteins.
[50] B Honig,et al. An algorithm to generate low-resolution protein tertiary structures from knowledge of secondary structure. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[51] Richard O. Duda,et al. Pattern classification and scene analysis , 1974, A Wiley-Interscience publication.
[52] M. Levitt,et al. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. , 1996, Journal of molecular biology.
[53] M J Sippl,et al. Progress in fold recognition , 1995, Proteins.
[54] D. Eisenberg,et al. A method to identify protein sequences that fold into a known three-dimensional structure. , 1991, Science.
[55] D Baker,et al. Local sequence-structure correlations in proteins. , 1996, Current opinion in biotechnology.
[56] K. Fidelis,et al. Comparison of systematic search and database methods for constructing segments of protein structure. , 1994, Protein engineering.
[57] J. Skolnick,et al. Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin , 1994, Proteins.
[58] T. Salakoski,et al. Selection of a representative set of structures from brookhaven protein data bank , 1992, Proteins.
[59] R. Srinivasan,et al. LINUS: A hierarchic procedure to predict the fold of a protein , 1995, Proteins.