A multi-expert system for the automatic detection of protein domains from sequence information

Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

Volumn , Issue , 2003, Pages 224-234

  Nagarajan, Niranjan ^a   Yona, Golan ^a  

^a NONE

Author keywords

Domain boundaries; Domain prediction; Protein domains; SCOP

Indexed keywords

ALGORITHMS; DATABASE SYSTEMS; DNA SEQUENCES; NEURAL NETWORKS; PROTEINS;

PROTEIN DOMAINS;

GENETIC ENGINEERING;

EID: 0037700981     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/640075.640104     Document Type: Conference Paper

References (43)

1. Rose, G. D. (1979). Hierarchic organization of domains in globular proteins. J. Mol. Biol. 134, 447-470.
2. Lesk, A. M. & Rose, G. D. (1981). Folding units in globular proteins. Proc. Natl. Acad. Sci. USA 78, 4304-4308.
3. Holm, L. & Sander, C. (1994). Parser for protein folding units. Proteins 19, 256-268.
4. Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
5. Yona, G. & Levitt, M. (2000). Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins. In the proceedings of ISMB 2000, 395-406, AAAI press, Menlo Park.
6. Kuroda, Y., Tani, K., Matsuo, Y. & Yokoyama, S. (2000). Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics. Protein Sci. 9, 2313-2321.
7. George, R. A. & Heringa, J. (2002). Protein domain identification and improved sequence similarity searching using PSI-BLAST. Proteins 48, 672-681.
8. Gouzy, J., Corpet, F. & Kahn, D. (1999). Whole genome protein domain analysis using a new method for domain clustering. Comput Chem. 23, 333-340.
9. Sonnhammer, E. L. L. & Kahn, D. (1994). Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 3, 482-492.
10. Park, J. & Teicmann, S. A. (1998). DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics 14:2, 144-150.
11. Gracy, J. & Argos, P. (1998). Automated protein sequence database classification. I. Integration of copositional similarity search, local similarity search and multiple sequence alignment. II. Delineation of domain boundries from sequence similarity. Bioinformatics 14:2, 164-187.
12. Sonnhammer, E. L., Eddy, S. R., Durbin, R. (1997). Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28, 405-420.
13. Bateman, A., Birney, E., Durbin, R., Eddy, S. R., Finn R. D., & Sonnhammer E. L. (1999). Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucl. Acids Res. 27, 260-262.
14. Haft, D. H., Loftus, B. J., Richardson, D. L., Yang, F., Eisen, J. A., Paulsen, I. T. & White, O. (2001). TIGRFAMs: a protein family resource for the functional identification of proteins. Nucl. Acids Res. 29, 41-43.
15. Ponting, C. P., Schultz, J., Milpetz, F. & Bork, P. (1999). SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucl. Acids Res. 27, 229-232.
16. George, R. A. & Heringa, J. (2002). SnapDRAGON: a method to delineate protein structural domains from sequence data. J. Mol. Biol. 316, 839-851.
17. Rigden, D. J. (2002). Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments. Protein Eng. 15, 65-77.
18. Guan, X. & Du, L. (1998). Domain identification by clustering sequence alignments. Bioinformatics 14, 783-788.
19. Wheelan, S. J., Marchler-Bauer, A. & Bryant, S. H. (2000). Domain size distributions can predict domain boundaries. Bioinformatics 16, 613-618.
20. George, D. G., Barker, W. C., Mewes, H. W., Pfeiffer, F. & Tsugita, A. (1996). The PIR-International protein sequence database. Nucl. Acids. Res. 24, 17-20.
21. Bairoch, A. & Apweiler, R. (1999). The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucl. Acids Res. 27 49-54.
22. Hubbard, T. J., Ailey, B., Brenner, S. E., Murzin, A. G. & Chothia, C. (1999). SCOP: a Structural Classification of Proteins database. Nucl. Acids Res. 27, 254-256.
23. Westbrook, J., Feng, Z., Jain, S. et al. (2002). The Protein Data Bank: unifying the archive. Nucl. Acids. Res. 30, 245-248
24. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389-3402.
25. Yona, G., Linial, N. & Linial, M. (1999). ProtoMap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins, 37, 360-378.
26. Henikoff, J. G. & Henikoff, S. (1996). Using substitution probabilities to improve position-specific scoring matrices. Comp. App. Biosci. 12:2, 135-143.
27. Hobohm, U. & Sander, C. (1995). A sequence property approach to searching protein database. J. Mol. Biol. 251, 390-399.
28. Ferran, E. A., Pflugfelder, B. & Ferrara P. (1994). Self-Organized Neural Maps of Human Protein Sequences. Protein Sci. 3, 507-521.
29. Csiszr, I. Information Theoretic Methods in Probability and Statistics. From citeseer.nj.nec.com
30. Henikoff, S. & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA 89, 10915-10919.
31. Pazos, F., Helmer-Citterich, M., Ausiello, G. & Valencia, A. (1997). Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271, 511-523.
32. Black, S.D. & Mould, D.R. (1991). Development of Hydrophobicity Parameters to Analyze Proteins Which Bear Post or Cotranslational Modifications. Anal. Biochem. 193, 72-82.
33. Sowdhamini, R. & Blundell, T. L. (1995). An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci. 4, 506-520.
34. McGuffin, L. J., Bryson, K. & Jones, D. T. (2000). The PSIPRED protein structure prediction server. Bioinformatics 16, 404-405.
35. Gilbert, W. & Glynias, M. (1993). On the ancient nature of introns. Gene 135, 137-144.
36. Gilbert, W., de Souza, S. J. & Long, M. (1997). Origin of genes. Proc. Natl Acad. Sci. USA 94, 7698-7703.
37. Saxonov, S. , Daizadeh, I. , Fedorov, A. & Gilbert, W. (2000). EID: the Exon-Intron Database-an exhaustive database of protein-coding intron-containing genes. Nucl. Acids Res. 28, 185-190.
38. Lin, J. (1991). Divergence measures based on the Shannon entropy. IEEE Trans. Info. Theory 37:1, 145-151.
39. Kullback, S. (1959). "Information theory and statistics". John Wiley and Sons, New York.
40. El-Yaniv, R., Fine, S. & Tishby, N. (1997). Agnostic classification of markovian sequences. Advances in Neural Information Processing Systems 10, 465-471.
41. Ireland, C. T. & Kullback, S. (1968). Contingency tables with given marginals. Biometrika 55, 179-189.
42. Pearl, J. (1997). "Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference." Morgan Kaufmann Publishers Inc.. San Mateo, California.
43. Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M. D., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A., Karavidopbulou, Y., Lopez, R., Marx, B., Mulder, N. J., Oinn, T. M., Pagni, M., Servant, F., Sigrist, C. J. & Zdobnov, E. M. (2001). The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucl. Acids Res. 29, 37-40.