PEP: Predictions for entire proteomes

Nucleic Acids Research

Volumn 31, Issue 1, 2003, Pages 410-413

  Carter, Phil ^a   Liu, Jinfeng ^a   Rost, Burkhard ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; PROTEOME; SIGNAL PEPTIDE;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; CELL FUNCTION; COMPUTER PREDICTION; EMBL NUCLEOTIDE SEQUENCE DATABASE; EUKARYOTE; HUMAN; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; PREDICTIONS FOR ENTIRE PROTEOMES; PRIORITY JOURNAL; PROKARYOTE; PROTEIN DATABASE; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SWISS-PROT;

ANIMALS; ARCHAEAL PROTEINS; CLUSTER ANALYSIS; DATABASES, PROTEIN; EUKARYOTIC CELLS; HUMANS; PROKARYOTIC CELLS; PROTEIN CONFORMATION; PROTEINS; PROTEOME; SEQUENCE HOMOLOGY, AMINO ACID; USER-COMPUTER INTERFACE;

ARCHAEA; EUKARYOTA; PROKARYOTA;

EID: 0037250635     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg102     Document Type: Review

References (22)

1. Rost,B. (2002) Did evolution leap to create the protein universe? Curr. Opin. Struct. Biol., 12, 409-416.
2. Liu,J. and Rost,B. (2001) Comparing function and structure between entire proteomes. Protein Sci., 10, 1970-1979.
3. Liu,J., Tan,H. and Rost,B. (2002) Loopy proteins appear conserved in evolution. J. Mol. Biol., 322, 53-64.
4. Liu,J. and Rost,B. (2002) Target space for structural genomics revisited. Bioinformatics, 18, 922-933.
5. Montelione,G.T. (2001) Structural genomics: an approach to the protein folding problem. Proc. Natl Acad. Sci. USA, 98, 13488-13489.
6. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TFEMBL in 2000. Nucleic Acids Res., 28, 45-48.
7. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
8. The Flybase Consortium (2002) The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res., 30, 106-108.
9. Stein,L., Sternberg,P., Durbin,R., Thierry-Mieg,J. and Spieth,J. (2001) WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res., 29, 82-86.
10. Altschul,S.F. and Gish,W. (1996) Local alignment statistics. Methods Enzymol., 266, 460-480.
11. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
12. Sander,C. and Schneider,R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
13. 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.
14. Lupas,A. (1996) Prediction and analysis of coiled-coil structures. Methods Enzymol., 266, 513-525.
15. Rost,B. (2001) Review: protein secondary structure prediction continues to rise. J. Struct. Biol., 134, 204-218.
16. Rost,B. (1996) PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol., 266, 525-539.
17. Wootton,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.
18. Nielsen,H., Engelbrecht,J., Brunak,S. and von Heijne,G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng., 10, 1-6.
19. Falquet,L., Pagni,M., Bucher,P., Hulo,N., Sigrist,C.J., Hofmann,K. and Bairoch,A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res., 30, 235-238.
20. Cokol,M., Nair,R. and Rost,B. (2000) Finding nuclear localization signals. EMBO Rep., 1, 411-415.
21. Nair,R., Carter,P. and Rost,B. (2003) NLSdb: database of nuclear localization signals. Nucleic Acids Res., 31, 342-344.
22. Etzold,T. and Argos,P. (1993) Transforming a set of biological flat file libraries to a fast access network. Comput. Appl. Biosci., 9, 49-57.