Template-based modeling and free modeling by I-TASSER in CASP7

Proteins: Structure, Function and Genetics

Volumn 69, Issue SUPPL. 8, 2007, Pages 108-117

  Zhang, Yang ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

CASP; Free modeling; I TASSER; Template refinement; Threading

Indexed keywords

AMINO ACID SEQUENCE; CONFERENCE PAPER; CRYSTAL STRUCTURE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENOME; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PEPTIDE LIBRARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 36749061828     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21702     Document Type: Conference Paper

References (47)

1. Terwilliger TC, Waldo G, Peat TS, Newman JM, Chu K, Berendzen J. Class-directed structure determination: foundation for a protein structure initiative. Protein Sci 1998;7:1851-1856.
2. Brenner SE, Levitt M. Expectations from structural genomics. Protein Sci 2000;9:197-200.
3. Stevens RC, Yokoyama S, Wilson IA. Global efforts in structural genomics. Science 2001;294:89-92.
4. Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
5. Skolnick J, Fetrow JS, Kolinski A. Structural genomics and its importance for gene function analysis. Nat Biotechnol 2000;18:283-287.
6. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
7. Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 2006;34:D291-D295.
8. Vitkup D, Melamud E, Moult J, Sander C. Completeness in structural genomics. Nat Struct Biol 2001;8:559-566.
9. Klebe G. Virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 2006;11:580-594.
10. Hubbard RE, editor. Structure-based drug discovery, 1st ed. Royal Society of Chemistry; Cambridge, UK, 2006.
11. Pal D, Eisenberg D. Inference of protein function from protein structure. Structure 2005;13:121-130.
12. Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
13. Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
14. Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004;101:7594-7599.
15. Tramontano A, Morea V. Assessment of homology-based predictions in CASP5. Proteins 2003;53(Suppl 6):352-368.
16. Tress M, Ezkurdia I, Grana O, Lopez G, Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins 2005;61(Suppl 7):27-45.
17. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209-225.
18. Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 2005;309:1868-1871.
19. Liwo A, Lee J, Ripoll DR, Pillardy J, Scheraga HA. Protein structure prediction by global optimization of a potential energy function. Proc Natl Acad Sci USA 1999;96:5482-5485.
20. Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 2003;85:1145-1164.
21. Wu ST, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 2007;5:17.
22. Zhang Y, Skolnick J. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J 2004;87:2647-2655.
23. Zhang Y, Arakaki A, Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 2005;61(Suppl 7):91-98.
24. Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Protein 2004;56:502-518.
25. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
26. Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
27. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J MoI Biol 1999;292:195-202.
28. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
29. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970;48:443-453.
30. Smith TF, Waterman MS. Identification of common molecular sub-sequences. J Mol Biol 1981;147:195-197.
31. Domingues FS, Lackner P, Andreeva A, Sippl MJ. Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J Mol Biol 2000;297:1003-1013.
32. Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 1997;6:676-688.
33. Chen H, Zhou HX. Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res 2005;33:3193-3199.
34. Zhang Y, Hubner I, Arakaki A, Shakhnovich E, Skolnick J. On the origin and completeness of highly likely single domain protein structures. Proc Natl Acad Sci USA 2006;103:2605-2610.
35. Swendsen RH, Wang JS. Replica Monte Carlo simulation of spin glasses. Phys Rev Lett 1986;57:2607-2609.
36. Zhang Y, Kihara D, Skolnick J. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins 2002;48:192-201.
37. Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004;25:865-871.
38. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302-2309.
39. Feig M, Rotkiewicz P, Kolinski A, Skolnick J, Brooks CL, III. Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models. Proteins 2000;41:86-97.
40. Canutescu AA, Shelenkov AA, Dunbrack RL, Jr. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
41. Kim DE, Chivian D, Malmstrom L, Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and Rosetta-DOM. Proteins 2005;61(Suppl 7):193-200.
42. Shi J, Blundell TL, Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001;310:243-257.
43. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005;21:951-960.
44. McGuffin LJ, Jones DT. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 2003;19:874-881.
45. Zhou H, Zhou Y. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 2005;58:321-328.
46. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004;57:702-710.
47. Cymborowski MT, Evdokimova E, Kagan O, Chruszcz M, Savchenko A, Edwards A, Minor W, Joachimiak A. Crystal structure of the protein RPA1889 from Rhodopseudomonas palustris CGA009, doi 10.2210/pdb2i9c/pdb.