A hypergraph-based method for unification of existing protein structure- and sequence-families

In Silico Biology

Volumn 2, Issue 3, 2002, Pages 339-349

  Freudenberg, Jan ^a,e   Zimmer, Ralf ^b,e   Hanisch, Daniel ^c,e   Lengauer, Thomas ^d,e  

^a UNIVERSITY HOSPITAL BONN   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

^c FRAUNHOFER INSTITUTE FOR ALGORITHMS AND SCIENTIFIC COMPUTING SCAI   (Germany)

^d MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^e FRAUNHOFER INSTITUTE FOR APPLIED INFORMATION TECHNOLOGY FIT   (Germany)

Author keywords

Domain boundary delineation; Optimization; Protein clustering; Protein databases; Protein homology; Protein structure prediction; Sequence analysis; Structure analysis; Template selection; Threading

Indexed keywords

4 HYDROXYPHENYLPYRUVATE DIOXYGENASE; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; BIOINFORMATICS; CLASSIFICATION; CLUSTER ANALYSIS; CONFERENCE PAPER; CONTROLLED STUDY; DATA BASE; DNA TEMPLATE; METHODOLOGY; NONHUMAN; PREDICTION; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; PSEUDOMONAS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION;

DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 0036455945     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (17)

1. Hadley, C. and Jones, D.T. (1999). A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure Fold Des. 7, 1099-1112.
2. Elofson, A. and Sonnhammer, E.L. (1999). A comparison of sequence and structure domain families as a basis for structural genomics. Bioinformatics 15, 480-500.
3. 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., Karavidopoulou, Y., Lopez, R., Marx, B., Mulder, N.J., Oinn, T.M., Pagni, M. and Servant, F. (2001). The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29, 37-40.
4. Pearl, F.M., Lee, D., Bray, J.E., Sillitoe, I., Todd, A.E., Harrison, A.P., Thornton, J.M. and Orengo, C.A. (2000). Assigning genomic sequences to CATH. Nucleic Acids Res. 28, 277-282.
5. Yona, G. and Levitt, M. (2000). Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8, 395-406.
6. Lang, D., Thoma, R., Henn-Sax, M., Sterner, R. and Wilmanns, M. (2000). Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science 289 1546-1549.
7. Hobohm, U. and Sander, C. (1994). Enlarged representative set of protein structures. Protein Sci. 3, 522-524.
8. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995). SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
9. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. and Thornton, J.M. (1997). CATH-A hierarchic classification of protein domain structures. Structure 5, 1093-1108.
10. Dietmann, S., Park, J., Notredame, C., Heger, A., Lappe, M. and Holm, L. (2001). A fully automatic evolutionary classification of protein folds: Dali Domain Classification version 3. Nucleic Acids Res. 29, 55-57.
11. Sonnhammer, E.L., Eddy, S.R., Birney, E., Bateman, A. and Durbin, R. (1998). Pfam: Multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 26, 320-322.
12. Schultz, J., Milpetz, F., Bork, P and Ponting, C.P. (1998). SMART, a simple modular architecture research tool: Identification of signaling domains. Proc. Natl. Acad. Sci. USA 95, 5857-5864.
13. Corpet, F., Servant, F., Gouzy, J. and Kahn, D. (2000). ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 28, 267-269.
14. Hofmann, K., Bucher, P., Falquet, L. and Bairoch, A. (1999). The PROSITE database. Nucleic Acids Res. 27, 215-219.
15. Attwood, T.K., Croning, M.D., Flower, D.R., Lewis, A.P., Mabey, J.E., Scordis, P., Selley, J.N. and Wright, W. (2000). PRINTS-S: The database formerly known as PRINTS. Nucleic Acids Res. 28, 225-227.
16. Karypis, G. and Kumar, V. hMETIS: A Hypergraph Partitioning Package. Technical Report, University of Minnesota, (1998).
17. Westhead, D.R., Slidel, T.W., Flores, T.P. and Thornton, J.M. (1999). Protein structural topology: Automated analysis and diagrammatic representation. Protein Sci. 8, 897-904.