UniqueProt: Creating representative protein sequence sets

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3789-3791

  Mika, Sven ^a,b   Rost, Burkhard ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b UNIVERSITY OF WITTEN HERDECKE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE CLUSTER; INFORMATION PROCESSING; INTERNET; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; SEQUENCE HOMOLOGY; ALGORITHM; CHEMISTRY; COMPUTER INTERFACE; METHODOLOGY; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

PROTEIN;

ALGORITHMS; INTERNET; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 0043122933     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg620     Document Type: Article

References (20)

1. Rost,B. (2002) Enzyme function less conserved than anticipated. J. Mol. Biol., 318, 595-608.
2. Todd,A.E., Orengo,C.A. and Thornton,J.M. (2001) Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol., 307, 1113-1143.
3. Nair,R. and Rost,B. (2002) Sequence conserved for sub-cellular localization. Protein Sci., 11, 2836-2847.
4. Tamames,J., Ouzounis,C., Casari,G., Sander,C. and Valencia,A. (1998) EUCLID: automatic classification of proteins in functional classes by their database annotations. Bioinformatics, 14, 542-543.
5. Devos,D. and Valencia,A. (2000) Practical limits of function prediction. Proteins, 41, 98-107.
6. Ashburner,M., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S. and Eppig,J.T. (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nature Genet., 25, 25-29.
7. Wilson,C.A., Kreychman,J. and Gerstein,M. (2000) Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol., 297, 233-249.
8. Brenner,S.E., Chothia,C. and Hubbard,T.J.P. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci. USA, 95, 6073-6078.
9. Rost,B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12, 85-94.
10. Yang,A.S. and Honig,B. (2000) An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. J. Mol. Biol., 301, 679-689.
11. Alexandrov,N.N. and Soloveyev,V.V. (1998) Statistical significance of ungapped sequence alignments. In Altman,R.B., DunkerA.K., Hunter,L. and Klein,T.E. (eds), HICCS 98: Pacific Symposium on Biocomputing 98. World Scientific, Maui, Hawaii, USA, pp. 463-472.
12. Sander,C. and Schneider,R. (1991) Database of homology-derived structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
13. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
14. Berman,H.M., Westbrook,J., Feng,Z., Gillliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
15. Altschul,S.F. and Gish,W. (1996) Local alignment statistics. Methods Enzymol., 266, 460-480.
16. Altschul,S., Madden,T., Shaffer,A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D. (1997) Gapped Blast and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
17. Hobohm,U. and Sander,C. (1994) Enlarged representative set of protein structures. Protein Sci., 3, 522-524.
18. Park,J., Teichmann,S.A., Hubbard,T. and Chothia,C. (1997) Intermediate sequences increase the detection of distant sequence homologies. J. Mol. Biol., 273, 349-354.
19. Enright,A.J. and Ouzounis,C.A. (2000) GeneRAGE: a robust algorithm for sequence clustering and domain detection. Bioinformatics, 16, 451-457.
20. Li,W., Jaroszewski,L. and Godzik,A. (2001) Clustering of highly homologous sequences to reduce the size of large profein databases. Bioinformatics, 17, 282-283.