SPARKS 2 and SP3 servers in CASP6

Proteins: Structure, Function and Genetics

Volumn 61, Issue SUPPL. 7, 2005, Pages 152-156

  Zhou, Hongyi ^a   Zhou, Yaoqi ^a,b  

^a UNIVERSITY AT BUFFALO   (United States)

^b FUDAN UNIVERSITY   (China)

Author keywords

Fold recognition; Protein structure prediction, sequence profile; Protein threading

Indexed keywords

ANALYTIC METHOD; COMPARATIVE STUDY; CONFERENCE PAPER; CRITICAL ASSESSMENT OF PROTEIN STRUCTURE PREDICTION METHOD; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEIN TARGETING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; ALGORITHM; ARTICLE; AUTOMATION; BIOLOGY; CHEMICAL STRUCTURE; COMPUTER; COMPUTER PROGRAM; COMPUTER SIMULATION; DIMERIZATION; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; PROTEOMICS; REPRODUCIBILITY;

ALGORITHMS; AUTOMATION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; COMPUTERS; DATABASES, PROTEIN; DIMERIZATION; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 30344456694     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20732     Document Type: Conference Paper

References (45)

1. Jones DT, Taylor WR, Thornton JM, A new approach to protein fold recognition. Nature 1992;358:86-89.
2. Dayhoff MO, Barker WC, Hunt LT. Establishing homologies in protein sequences. Methods Enzymol 1983;91:524-545.
3. Pearson WR, Lipman DJ. Improved tools for biological sequence analysis. Proc Natl Acad Sci USA 1988;85:2444-2448.
4. Altschul SF, Gish W, Miller W, Myers E, Lipman D. Basic local alignment tool. J Mol Biol 1990;215:403-410.
5. Vingron M, Waterman MS. Sequence alignment and penalty choice: review of concepts, case studies and implications. J Mol Biol 1994;235:1-12.
6. Qian B, Goldstein RA. Optimization of a new score function for the generation of accurate alignments. Proteins 2002;48:605-610.
7. Teodorescu O, Galor T, Pillardy J, Elber R. Enriching the sequence substitution matrix by structural information. Proteins 2004;54:41-48.
8. Altschul SF, Madden TL, Schäffer 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.
9. Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
10. Henikoff S, Henikoff JG. Amino acid substitutes matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915-10919.
11. Bailey TL, Gribskov M. Score distributions for simultaneous matching to multiple motifs. J Comput Biol 1997;4:45-59.
12. Koretke KK, Russell RB, Lupas AN. Fold recognition from sequence comparisons. Proteins 2001;Suppl 5:68-75.
13. Eddy SR. Profile hidden Markov models. Bioinformatics 1998;14:755-763.
14. Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci USA 1987;84:4355-4358.
15. Rychlewski L, Jaroszewski L, Li W, Gudzik A. Comparison of sequence profiles: strategies for structural predictions using sequence information. Protein Sci 2000;9:232-241.
16. Yona G, Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol 2002;315:1257-1275.
17. Marti-Renom MA, Madhusudhan M, Sali A. Alignment of protein sequences by their profiles. Protein Sci 2004;13:1071-1087.
18. Bowie JW, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
19. Gudzik A, Skolnick J. Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. Proc Natl Acad Sci USA 1992;89:12098-12102.
20. Bryant SH, Lawrence CE. An empirical energy function for threading protein sequence through the folding motif. Proteins 1993;16:92-112.
21. Abagyan R, Frishman D, Argos P. Recognition of distantly related proteins through energy calculations. Proteins 1994;19:132-140.
22. Murzin AG, Bateman A. Distance homology recognition using structural classification of proteins. Proteins 1997;Suppl 1:105-112.
23. Xu Y, Xu D. Protein threading using PROSPECT: design and evaluation. Proteins 2000;40:343-354.
24. Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR-a new approach to threading. Proteins 2001;42:319-331.
25. Yi TM, Lander ES. Recognition of related proteins by iterative template refinement (ITR). Protein Sci 1994;3:1315-1328.
26. Elofsson A, Fischer D, Rice DW, Le Grand SM, Eisenberg D. A study of combined structure/sequence profiles. Fold Des 1996;1:451-461.
27. Fischer D, Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci 1996;5:947-955.
28. Rost B, Sander C. Protein fold recognition by prediction-based threading. J Mol Biol 1997;270:471-480.
29. Jaroszewski L, Rychlewski L, Zhang B, Godzik A. Fold prediction by a hierarchy of sequence, threading, and modeling methods. Protein Sci 1998;7:1431-1440.
30. Kelley LA, MacCallum RM, Sternberg MJE. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000;299:499-520.
31. Panchenko AR, Marchler-Bauer A, Bryant SH. Combination of threading potentials and sequence profiles improves fold recognition. J Mol Biol 2000;296:1319-1331.
32. Shan YB, Wang GL, Zhou HX. Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading. Proteins 2001;42:23-37.
33. Al-Lazikani B, Sheinerman FB, Honig B. Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases. Proc Natl Acad Sci USA 2001;98:14796-14801.
34. Kim D, Xu D, Guo J, Ellrott K, Xu Y. PROSPECT II: protein structure prediction program for the genome-scale. Protein Eng 2003;16:641-650.
35. Tang CL, Xie L, Koh IY, Posy S, Alexov E, Honig B. On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol 2003;334:1043-1062.
36. Zhou H, Zhou Y. Single-body knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004;55:1005-1013.
37. Godzik A. Fold recognition methods. Methods Biochem Anal 2003;44:525-546.
38. 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.
39. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981;147:195-197.
40. 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.
41. Marti-Renom M, Stuart A, Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000;29:291-325.
42. Available online at http://predictioncenter.org/casp6/abstracts/ CASP6_Tables_light.txt
43. Zhang Y, Skolnick J. Available online at http://www.bioinformatics. buffalo.edu/new_buffalo/people/zhang6/casp6/
44. Zhang Y, Skolnick J. Scoring function for the automated assessment of protein structure template quality. Proteins 2004;57:702-710.
45. Shindyalov IN, Bourne P. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998;11:739-747.