A historical perspective of template-based protein structure prediction.
暂无分享,去创建一个
Ying Xu | Kyle Ellrott | Jun-Tao Guo | Jun-tao Guo | Ying Xu | K. Ellrott
[1] M J Sternberg,et al. Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM , 2001, Proteins.
[2] H. Scheraga,et al. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. , 1976, Macromolecules.
[3] I. Lasters,et al. Fast and accurate side‐chain topology and energy refinement (FASTER) as a new method for protein structure optimization , 2002, Proteins.
[4] David C. Jones,et al. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. , 1999, Journal of molecular biology.
[5] M. Levitt,et al. Computer simulation of protein folding , 1975, Nature.
[6] 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.
[7] R. Samudrala,et al. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. , 1998, Journal of molecular biology.
[8] J Bajorath,et al. Identification of residues on CD40 and its ligand which are critical for the receptor-ligand interaction. , 1995, Biochemistry.
[9] A. Lesk,et al. The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.
[10] Richard Hughey,et al. Hidden Markov models for detecting remote protein homologies , 1998, Bioinform..
[11] S. Altschul,et al. Issues in searching molecular sequence databases , 1994, Nature Genetics.
[12] Woei-Jyh Lee,et al. Evaluation of domain prediction in CASP6 , 2005, Proteins.
[13] D. Baker,et al. Protein structure prediction in 2002. , 2002, Current opinion in structural biology.
[14] M J Sippl,et al. Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.
[15] Ceslovas Venclovas,et al. Progress over the first decade of CASP experiments , 2005, Proteins.
[16] M. Levitt. A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.
[17] M. Levitt. Accurate modeling of protein conformation by automatic segment matching. , 1992, Journal of molecular biology.
[18] Y. Matsuo,et al. Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. , 1993, Protein engineering.
[19] J. Skolnick,et al. TOUCHSTONE II: a new approach to ab initio protein structure prediction. , 2003, Biophysical journal.
[20] M J Sippl,et al. Assessment of the CASP4 fold recognition category , 2001, Proteins.
[21] Zhexin Xiang,et al. Homology-Based Modeling of Protein Structure , 2007 .
[22] M. Levitt,et al. A unified statistical framework for sequence comparison and structure comparison. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[23] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[24] 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.
[25] J F Riordan,et al. A preliminary three-dimensional structure of angiogenin. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[26] A. Godzik,et al. Comparison of sequence profiles. Strategies for structural predictions using sequence information , 2008, Protein science : a publication of the Protein Society.
[27] Roland L. Dunbrack,et al. CAFASP3: The third critical assessment of fully automated structure prediction methods , 2003, Proteins.
[28] Janet M. Thornton,et al. Protein fold recognition , 1993, J. Comput. Aided Mol. Des..
[29] C. Levinthal,et al. Predicting antibody hypervariable loop conformations II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations , 1986, Proteins.
[30] J. Ponder,et al. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.
[31] D T Jones,et al. Prediction of novel and analogous folds using fragment assembly and fold recognition , 2005, Proteins.
[32] Yang Zhang,et al. TASSER: An automated method for the prediction of protein tertiary structures in CASP6 , 2005, Proteins.
[33] Y Xu,et al. Protein threading using PROSPECT: Design and evaluation , 2000, Proteins.
[34] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[35] P Argos,et al. An assessment of protein secondary structure prediction methods based on amino acid sequence. , 1976, Biochimica et biophysica acta.
[36] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[37] Jinbo Xu,et al. Rapid Protein Side-Chain Packing via Tree Decomposition , 2005, RECOMB.
[38] A. D. McLachlan,et al. Solvation energy in protein folding and binding , 1986, Nature.
[39] Hongyi Zhou,et al. Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition , 2004, Proteins.
[40] Lisa N Kinch,et al. CASP5 assessment of fold recognition target predictions , 2003, Proteins.
[41] T. L. Blundell,et al. Knowledge-based prediction of protein structures and the design of novel molecules , 1987, Nature.
[42] A. Sali,et al. Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.
[43] S. Bryant,et al. Statistics of sequence-structure threading. , 1995, Current opinion in structural biology.
[44] Steven E Brenner,et al. The Impact of Structural Genomics: Expectations and Outcomes , 2005, Science.
[45] K Fidelis,et al. A large‐scale experiment to assess protein structure prediction methods , 1995, Proteins.
[46] David C. Jones,et al. Potential energy functions for threading. , 1996, Current opinion in structural biology.
[47] K. Fidelis,et al. Comparison of systematic search and database methods for constructing segments of protein structure. , 1994, Protein engineering.
[48] D T Jones,et al. Protein fold recognition by sequence threading: tools and assessment techniques , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[49] Daniel Fischer,et al. ‘Meta’Approaches to Protein Structure Prediction , 2008 .
[50] J. Jung,et al. Protein structure prediction. , 2001, Current opinion in chemical biology.
[51] Shoji Takada,et al. A Reversible Fragment Assembly Method for De Novo Protein Structure Prediction , 2003 .
[52] B Contreras-Moreira,et al. Empirical limits for template‐based protein structure prediction: the CASP5 example , 2005, FEBS letters.
[53] I Lasters,et al. Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains. , 1995, Protein engineering.
[54] Julian Lee,et al. PROTEINS: Structure, Function, and Bioinformatics 56:704–714 (2004) Prediction of Protein Tertiary Structure Using PROFESY, a Novel Method Based on Fragment Assembly and , 2022 .
[55] Liam J. McGuffin,et al. Improvement of the GenTHREADER Method for Genomic Fold Recognition , 2003, Bioinform..
[56] Akbar Nayeem,et al. A comparative study of available software for high‐accuracy homology modeling: From sequence alignments to structural models , 2006, Protein science : a publication of the Protein Society.
[57] David Baker,et al. Protein Structure Prediction Using Rosetta , 2004, Numerical Computer Methods, Part D.
[58] S F Altschul,et al. Local alignment statistics. , 1996, Methods in enzymology.
[59] J. Wójcik,et al. New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. , 1999, Journal of molecular biology.
[60] Hongyi Zhou,et al. Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments , 2004, Proteins.
[61] Golan Yona,et al. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. , 2002, Journal of molecular biology.
[62] T. A. Jones,et al. Using known substructures in protein model building and crystallography. , 1986, The EMBO journal.
[63] John Moult,et al. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. , 2005, Current opinion in structural biology.
[64] Thomas Lengauer,et al. Confidence measures for protein fold recognition , 2002, Bioinform..
[65] B. Honig,et al. A hierarchical approach to all‐atom protein loop prediction , 2004, Proteins.
[66] Janusz M Bujnicki,et al. Protein‐Structure Prediction by Recombination of Fragments , 2006, Chembiochem : a European journal of chemical biology.
[67] Barry Honig,et al. Extending the accuracy limits of prediction for side-chain conformations. , 2001 .
[68] Roland L Dunbrack,et al. Assessment of fold recognition predictions in CASP6 , 2005, Proteins.
[69] Dong Xu,et al. PROSPECT II: protein structure prediction program for genome-scale applications. , 2003, Protein engineering.
[70] J. Thompson,et al. 2 A crystal structure of an extracellular fragment of human CD40 ligand. , 1995, Structure.
[71] D. Shortle,et al. Structure prediction: The state of the art , 1999, Current Biology.
[72] T. Blundell,et al. Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. , 1987, Protein engineering.
[73] C. Murray,et al. Protein fold recognition by threading: comparison of algorithms and analysis of results. , 1995, Protein engineering.
[74] J Bajorath,et al. Detailed Comparison of Two Molecular Models of the Human CD40 Ligand with an X-ray Structure and Critical Assessment of Model-based Mutagenesis and Residue Mapping Studies* , 1998, The Journal of Biological Chemistry.
[75] W. C. Ripka,et al. Computer-assisted model building , 1986, Nature.
[76] Roland L. Dunbrack,et al. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.
[77] G. N. Ramachandran,et al. Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins. , 2009, International journal of protein research.
[78] J Lundström,et al. Pcons: A neural‐network–based consensus predictor that improves fold recognition , 2001, Protein science : a publication of the Protein Society.
[79] C. Chothia. One thousand families for the molecular biologist , 1992, Nature.
[80] N. Isaacs,et al. Relaxin and its structural relationship to insulin , 1978, Nature.
[81] Yaoqi Zhou,et al. SPARKS 2 and SP3 servers in CASP6 , 2005, Proteins.
[82] Ying Xu,et al. PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction , 2004, Nucleic Acids Res..
[83] S. Wodak,et al. Modelling the polypeptide backbone with 'spare parts' from known protein structures. , 1989, Protein engineering.
[84] Anna Tramontano,et al. Ten years of predictions … and counting , 2005, The FEBS journal.
[85] D Xu,et al. Application of PROSPECT in CASP4: Characterizing protein structures with new folds , 2001, Proteins.
[86] J. Richardson,et al. The penultimate rotamer library , 2000, Proteins.
[87] Bonnie Berger,et al. A tree-decomposition approach to protein structure prediction , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).
[88] C DeLisi,et al. Estimating the number of protein folds. , 1998, Journal of molecular biology.
[89] Arne Elofsson,et al. Profile–profile methods provide improved fold‐recognition: A study of different profile–profile alignment methods , 2004, Proteins.
[90] David C. Jones,et al. CATH--a hierarchic classification of protein domain structures. , 1997, Structure.
[91] J. Skolnick,et al. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement , 2001, Proteins.
[92] C. Zhang,et al. Relations of the numbers of protein sequences, families and folds. , 1997, Protein engineering.
[93] S. Wodak,et al. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. , 1994, Journal of molecular biology.
[94] S. Karlin,et al. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[95] J. Greer,et al. Model structure for the inflammatory protein C5a. , 1985, Science.
[96] Johan Desmet,et al. The dead-end elimination theorem and its use in protein side-chain positioning , 1992, Nature.
[97] W. Pearson. Empirical statistical estimates for sequence similarity searches. , 1998, Journal of molecular biology.
[98] J. Straub,et al. Orientational potentials extracted from protein structures improve native fold recognition , 2004, Protein science : a publication of the Protein Society.
[99] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[100] C Kooperberg,et al. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.
[101] J L Sussman,et al. A 3D building blocks approach to analyzing and predicting structure of proteins , 1989, Proteins.
[102] Shoji Takada,et al. SimFold energy function for de novo protein structure prediction: Consensus with Rosetta , 2005, Proteins.
[103] J. Moult,et al. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search , 1986, Proteins.
[104] A. Godzik,et al. Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[105] E. Shakhnovich,et al. SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence , 1996 .
[106] Celia W G van Gelder,et al. A molecular dynamics approach for the generation of complete protein structures from limited coordinate data , 1994, Proteins.
[107] C Sander,et al. Mapping the Protein Universe , 1996, Science.
[108] B. Matthews. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. , 1975, Biochimica et biophysica acta.
[109] Adrian A Canutescu,et al. A graph‐theory algorithm for rapid protein side‐chain prediction , 2003, Protein science : a publication of the Protein Society.
[110] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[111] K Seyama,et al. Classification of mutations in the human CD40 ligand, gp39, that are associated with X‐linked hyper IgM syndrome , 1996, Protein science : a publication of the Protein Society.
[112] Hongyi Zhou,et al. The dependence of all-atom statistical potentials on structural training database. , 2004, Biophysical journal.
[113] Ying Xu,et al. Raptor: Optimal Protein Threading by Linear Programming , 2003, J. Bioinform. Comput. Biol..
[114] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[115] M J Sippl,et al. Progress in fold recognition , 1995, Proteins.
[116] Liam J McGuffin,et al. Assembling novel protein folds from super‐secondary structural fragments , 2003, Proteins.
[117] Robert L Jernigan,et al. How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins? , 2005, The Journal of chemical physics.
[118] David C. Jones. Predicting novel protein folds by using FRAGFOLD , 2001, Proteins.
[119] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[120] 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.
[121] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[122] D Fischer,et al. CAFASP‐1: Critical assessment of fully automated structure prediction methods , 1999, Proteins.
[123] Kentaro Shimizu,et al. Development of an ab initio protein structure prediction system ABLE. , 2003, Genome informatics. International Conference on Genome Informatics.
[124] Guoli Wang,et al. PISCES: a protein sequence culling server , 2003, Bioinform..
[125] J. Skolnick,et al. A distance‐dependent atomic knowledge‐based potential for improved protein structure selection , 2001, Proteins.
[126] Jonathan Casper,et al. Combining local‐structure, fold‐recognition, and new fold methods for protein structure prediction , 2003, Proteins.
[127] T L Blundell,et al. Knowledge based modelling of homologous proteins, Part II: Rules for the conformations of substituted sidechains. , 1987, Protein engineering.
[128] David C. Jones,et al. Progress in protein structure prediction. , 1997, Current opinion in structural biology.
[129] D C Richardson,et al. Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[130] Roland L Dunbrack,et al. Scoring profile‐to‐profile sequence alignments , 2004, Protein science : a publication of the Protein Society.
[131] Dong Xu,et al. Improving the performance of DomainParser for structural domain partition using neural network. , 2003, Nucleic acids research.
[132] T L Blundell,et al. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. , 2001, Journal of molecular biology.
[133] Ruben Recabarren,et al. Estimating the total number of protein folds , 1999, Proteins.
[134] A. Sali,et al. Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.
[135] D. T. Jones,et al. A new approach to protein fold recognition , 1992, Nature.
[136] Gary D. Stormo,et al. Phylogenetically enhanced statistical tools for RNA structure prediction , 2000, Bioinform..
[137] M Levitt,et al. The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure , 1986, Science.
[138] J Bajorath,et al. Analysis of gp39/CD40 interactions using molecular models and site-directed mutagenesis. , 1995, Biochemistry.
[139] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[140] R A Goldstein,et al. Why are some proteins structures so common? , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[141] B. L. Sibanda,et al. Three-dimensional structure, specificity and catalytic mechanism of renin , 1983, Nature.
[142] C. D. Barry,et al. Comparison of predicted and experimentally determined secondary structure of adenyl kinase , 1974, Nature.
[143] S. L. Mayo,et al. Conformational splitting: A more powerful criterion for dead‐end elimination , 2000, J. Comput. Chem..
[144] M J Sippl,et al. Threading thrills and threats. , 1996, Structure.
[145] C. Sander,et al. Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. , 1991, Journal of molecular biology.
[146] A. Sali,et al. Structural genomics: beyond the Human Genome Project , 1999, Nature Genetics.
[147] A. Godzik,et al. Topology fingerprint approach to the inverse protein folding problem. , 1992, Journal of molecular biology.
[148] J. Greer,et al. Model for haptoglobin heavy chain based upon structural homology. , 1980, Proceedings of the National Academy of Sciences of the United States of America.
[149] T. Blundell,et al. Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.
[150] M C Peitsch,et al. A 3-D model for the CD40 ligand predicts that it is a compact trimer similar to the tumor necrosis factors. , 1993, International immunology.
[151] G Kolata. Trying to crack the second half of the genetic code. , 1986, Science.
[152] J. Greer. Comparative model-building of the mammalian serine proteases. , 1981, Journal of molecular biology.
[153] B Honig,et al. Sequence to structure alignment in comparative modeling using PrISM , 1999, Proteins.
[154] N. Grishin,et al. Practical lessons from protein structure prediction , 2005, Nucleic acids research.
[155] David T. Jones. Successful ab initio prediction of the tertiary structure of NK‐lysin using multiple sequences and recognized supersecondary structural motifs , 1997, Proteins.
[156] I Lasters,et al. Theoretical and algorithmical optimization of the dead-end elimination theorem. , 1997, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[157] R. Lathrop. The protein threading problem with sequence amino acid interaction preferences is NP-complete. , 1994, Protein engineering.
[158] David T. Jones,et al. Protein superfamilles and domain superfolds , 1994, Nature.
[159] I. Lasters,et al. The fuzzy-end elimination theorem: correctly implementing the side chain placement algorithm based on the dead-end elimination theorem. , 1993, Protein engineering.
[160] T L Blundell,et al. Insulin-like growth factor: a model for tertiary structure accounting for immunoreactivity and receptor binding. , 1978, Proceedings of the National Academy of Sciences of the United States of America.
[161] Arne Elofsson,et al. All are not equal: A benchmark of different homology modeling programs , 2005, Protein science : a publication of the Protein Society.
[162] 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.
[163] M. Karplus,et al. PDB-based protein loop prediction: parameters for selection and methods for optimization. , 1997, Journal of molecular biology.
[164] R. Goldstein. Efficient rotamer elimination applied to protein side-chains and related spin glasses. , 1994, Biophysical journal.
[165] Lei Xie,et al. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling , 2003, Proteins.
[166] Z. X. Wang,et al. A re-estimation for the total numbers of protein folds and superfamilies. , 1998, Protein engineering.
[167] Ming Li,et al. Assessment of RAPTOR's linear programming approach in CAFASP3 , 2003, Proteins.
[168] Cinque S. Soto,et al. Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[169] M. Levitt,et al. Small libraries of protein fragments model native protein structures accurately. , 2002, Journal of molecular biology.
[170] S. Bryant,et al. An empirical energy function for threading protein sequence through the folding motif , 1993, Proteins.
[171] Z. X. Wang,et al. How many fold types of protein are there in nature? , 1996, Proteins.
[172] Jinbo Xu. Fold recognition by predicted alignment accuracy , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.