Automated data-driven discovery of motif-based protein function classifiers

Information Sciences

Volumn 155, Issue 1-2, 2003, Pages 1-18

  Wang, Xiangyun ^a   Schroeder, Diane ^a   Dobbs, Drena ^a   Honavar, Vasant ^a  

^a Iowa State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATION; CLASSIFICATION (OF INFORMATION); DECISION MAKING; DNA SEQUENCES; TREES (MATHEMATICS);

PROTEIN FUNCTION CLASSIFIERS;

PROTEINS;

EID: 0042235504     PISSN: 00200255     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0020-0255(03)00067-7     Document Type: Article

References (40)

1. Altschul S.F., Madden T.L., Schaffer A.A., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
2. Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D.R., Durbin R., Falquet L., Fleishchmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J.A., Zdobnov E.M. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29:2001;37-40.
3. Attwood T.K., Croning M.D.R., Flower D.R., Lewis A.P., Mabey J.E., Scordis P., Selley J., Wright W. PRINT-S: the database formerly known as PRINTS. Nucleic Acids Res. 28:2000;225-227 http://bioinf.man.ac.uk/dbbrowser/prints/.
4. Bailey T.L., Baker M.E., Elkan C.P., Grundy W.N. MEME, MAST, and Meta-MEME: new tools for motif discovery in protein sequences. Pattern Discovery in Biomolecular Data. 1999;30-54 Oxford University Press, Oxford.
5. Baker D., Sali A. Protein structure prediction and structural genomics. Science. 294:2001;93-96.
6. Baldi P.F., Brunak S. Bioinformatics: The Machine Learning Approach. 2001;The MIT Press, Cambridge, MA.
7. Barker W.C., Garavelli J.C., Hou Z., Huang H., Ledley R.S., McGarvey M.P., Mewes H.W., Orcutt B.C., Pfeiffer F., Tsugita A., Vinayaka C.R., Xiao C., Yeh L.L., Cathy Wu. Protein information resource: a community resource for expert annotation of protein data. Nucleic Acids Res. 29:2001;29-32 http://pir.georgetown.edu/.
8. Barrett A.J., Rawlings N.D., Woessner J.F. Handbook of Proteolytic Enzymes. 1998;Academic Press, New York.
9. Bateman A., Birney E., Durbin R., Eddy S.R., Howem K.L., Sonnhammer E.L.L. The Pfam protein families database. Nucleic Acids Res. 28:2000;263-266.
10. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Res. 28:2000;235-242 http://www.rcsb.org/pdb/.
11. Bond J.S., Beynon R.J. The astacin family of metalloendopeptidases. Protein Sci. 4:1995;1247-1261.
12. Bork P., Ouzounis C., Sander C. From genome sequences to protein function. Curr. Opin. Struct. Biol. 4:1994;393-403.
13. Chothia C., Gerstein M. Protein evolution. How far can sequences diverge? Nature. 85(6617):1997;579-581.
14. Chothia C., Lesk A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5(4):1986;823-826.
15. Dayhoff M.O., Barker W.C., Hunt L.T. Establishing homologies in protein sequences. Methods Enzymol. 91:1983;524.
16. Earnshaw W.C., Martins L.M., Kaufmann S.H. Mammalian caspases: structure, activation, substrates, and functions durng apoptosis. Annu. Rev. Biochem. 68:1999;383-424.
17. Eisenberg D., Marcotte E.M., Xenarios I., Yeates T.O. Protein function in the post-genomic era. Nature. 405(6788):2000;823-826.
18. Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J., Hofmann K., Bairoch A. The PROSITE database, its status in 2002. Nucleic Acids Res. 30:2002;235-238 http://www.expasy.ch/prosite/.
19. Fetrow J.S., Siew N., Di Gennaro J.A., Martinez-Yamout M., Dyson H.J., Skolnick J. Genomic-scale comparison of sequence- and structure-based methods of functionprediction: does structure provide additional insight? Protein Sci. 10(5):2001;1005-1014 Holm L., Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res. 25(1):1997;231-234.
20. Fetrow J.S., Siew N., Di Gennaro J.A., Martinez-Yamout M., Dyson H.J., Skolnick J. Genomic-scale comparison of sequence- and structure-based methods of functionprediction: does structure provide additional insight? Protein Sci. 10(5):2001;1005-1014 Holm L., Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res. 25(1):1997;231-234.
21. Henikoff J.G., Greene E.A., Pietrokovski S., Henikoff S. Increased coverage of protein families with the blocks database servers. Nucl. Acids Res. 28:2000;228-230.
22. Holm L., Sander C. Mapping the protein universe. Science. 273:1996;595-602.
23. Hudak J., McClure M.A. A comparative analysis of computational motif detection methods. Pacific Symp. Biocomput. 4:1999;138-149.
24. Jaakkola T., Diekhans M., Haussler D. A discriminative framework for detecting remote protein homologies. J. Comp. Biol. 7:2000;95-114.
25. King R.D., Karwath A., Clare A., Dehaspe L. The utility of different representations of protein sequence for predicting functional class. Bioinformatics. 17:2001;445-454.
26. Lo Conte L., Ailey B., Hubbard T.J., Brenner S.E., Murzin A.G., Chothia C. SCOP: a structural classification of proteins database. Nucleic Acids Res. 28(1):2000;257-259.
27. Mitchell T. Machine Learning. 1997;McGraw Hill, New York.
28. Neuwald A.F., Liu J.S., Lawrence C.E. Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci. 4:1995;1618-1632.
29. Orengo C.A., Todd A.E., Thornton J.M. From protein structure to function. Curr. Opin. Struct. Biol. 9(3):1999;374-382.
30. Pearl F.M., Martin N., Bray J.E., Buchan D.W., Harrison A.P., Lee D., Reeves G.A., Shepherd A.J., Sillitoe I., Todd A.E., Thornton J.M., Orengo C.A. A rapid classification protocol for the CATH Domain Database to support structural genomics. Nucleic Acids Res. 29(1):2001;223-227.
31. Pearson W.R. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol. 132:2000;185-219.
32. Quinlan J.R. C4.5: Programs for Machine Learning. 1992;Morgan Kaufmann, San Mateo, CA.
33. Rawlings N.D., Barrett A.J. MEROPS: the peptidase database. Nucleic Acids Res. 28:2002;323-325 http://www.merops.co.uk/.
34. Rigoutsos I., Floratos A., Ouzounis C., Gao Y., Parida L. Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins. Proteins. 37(2):1999;264-277.
35. Rost B. Twilight zone of protein sequence alignments. Protein Eng. 12(2):1999;85-94.
36. Samudrala R., Xia Y., Levitt M., Huang E.S. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pacific Symp. Biocomput. 4:1999;505-516.
37. Silverstein K.A.T., Shoop E., Johnson J.E., Retzel E.F. MetaFam: a unified classification of protein families. I. Overview and statistics. Bioinformatics. 17:2001;249-261.
38. Skolnick J., Fetrow J.S. From genes to protein structure and function: novel applications of computational approaches in the genomic era. Trends Biotechnol. 18(1):2000;34-39.
39. D. Wang, X. Wang, V. Honavar, D. Dobbs, Data-driven generation of decision trees for motif-based assignment of protein sequences to functional families, in: Proceedings of the Atlantic Symposium on Computational Biology, Genome Information Systems & Technology, 2001.
40. Wilson K.P., Black J.F., Thomson J.A., Kim E.E., Griffith J.P., Navia M.A., Murcko M.A., Chambers S.P., Aldape R.A., Raybuck S.A., Livingston D.J. Structure and mechanism of Interleukin-1β converting enzyme. Nature. 370:1994;270-275.