The iProClass integrated database for protein functional analysis

Computational Biology and Chemistry

Volumn 28, Issue 1, 2004, Pages 87-96

  Wu, Cathy H ^a   Huang, Hongzhan ^a   Nikolskaya, Anastasia ^a   Hu, Zhangzhi ^b   Barker, Winona C ^b  

^a GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

^b National Biomedical Research Foundation   (United States)

Author keywords

Bioinformatics; Human genome; Protein functional analysis

Indexed keywords

BACTERIA; BIOCHEMISTRY; BIOTECHNOLOGY; CLASSIFICATION (OF INFORMATION); DATA REDUCTION; DISTRIBUTED DATABASE SYSTEMS; GENES; METABOLISM; METADATA;

BIOINFORMATICS; HUMAN GENOME; PROTEIN FUNCTIONAL ANALYSIS;

PROTEINS;

PHOSPHOGLYCERATE MUTASE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMISTRY; FACTUAL DATABASE; GENETICS; GENOME; HUMAN; METABOLISM; METHODOLOGY; MOLECULAR BIOLOGY; MOLECULAR GENETICS; PHYLOGENY;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; GENOME, HUMAN; HUMANS; MOLECULAR BIOLOGY; MOLECULAR SEQUENCE DATA; PHOSPHOGLYCERATE MUTASE; PHYLOGENY; PROTEINS;

EID: 0842330093     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2003.10.003     Document Type: Note

References (37)

1. Achard F., Cussat-Blanc C., Viara E., Barillot E. The new Virgil database: a service of rich links. Bioinformatics. 14:1998;342-348.
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
3. Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Gasteiger, E., Huang, H., Martin, M.J., Natale, D.A., O'Donovan, C., Yeh, L.-S., 2004. UniProt: universal protein knowledgebase. Nucleic Acids Res. 32, (in press).
4. Babnigg G., Giometti C.S. ProteomeWeb: a web-based interface for the display and interrogation of proteomes. Proteomics. 3:2003;584-600.
5. Barker W.C., Pfeiffer F., George D.G. Superfamily classification in PIR-international protein sequence database. Methods Enzymol. 266:1996;59-71.
6. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., Griffiths-Jones S., Howe K.L., Marshall M., Sonnhammer E. The Pfam protein families database. Nucleic Acids Res. 30:2002;276-280.
7. Baxevanis A.D. The molecular biology database collection: 2003 update. Nucleic Acids Res. 31:2003;1-12.
8. Bond C.S., White M.F., Hunter W.N. Mechanistic implications for Escherichia coli cofactor-dependent phosphoglycerate mutase based on the high-resolution crystal structure of a vanadate complex. J. Mol. Biol. 316:2002;1071-1081.
9. Bono H., Nikaido I., Kasukawa T., Hayashizaki Y., Okazaki Y. Comprehensive analysis of the mouse metabolome based on the transcriptome. Genome Res. 13:2003;1345-1349.
10. Carninci P., Waki K., Shiraki T., Konno H., Shibata K., Itoh M., Hayashizaki Y. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res. 13:2003;1273-1289.
11. Davidson S.B., Overton C., Nuneman P. Challenges in integrating biological data sources. J. Comp. Biol. 2:1995;557-572.
12. Dayhoff M.O. The origin and evolution of protein superfamilies. Fed. Proc. 35:1976;2132-2138.
13. Dobson C.M., Wai T., Leclerc D., Kadir H., Narang M., Lerner-Ellis J.P., Hudson T.J., Rosenblatt D.S., Gravel R.A. Identification of the gene responsible for the cblB complementation group of vitamin B12-dependent methylmalonic aciduria. Hum. Mol. Genet. 11:2002;3361-3369.
14. Fenton W.A., Rosenberg L.E. The defect in the cbl B class of human methylmalonic acidemia: deficiency of cob(I)alamin adenosyltransferase activity in extracts of cultured fibroblasts. Biochem. Biophys. Res. Commun. 98:1981;283-289.
15. Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., Kanehisa, M., 1998. DBGET/LinkDB: an integrated database retrieval system. Pac. Symp. Biocomput. 683-694.
16. Gene Ontology Consortium, 2001. Creating the gene ontology resource: design and implementation. Genome Res. 11, 1425-1433.
17. Huang H., Barker W.C., Chen Y., Wu C.H. iProClass: an integrated database of protein family function and structure information. Nucleic Acids Res. 31:2003;390-392.
18. Hunter P.J., Borg T.K. Integration from proteins to organs: the Physiome Project. Nat. Rev. Mol. Cell Biol. 4:2003;237-243.
19. Johnson C.L., Pechonick E., Park S.D., Havemann G.D., Leal N.A., Bobik T.A. Functional genomic, biochemical, and genetic characterization of the Salmonella pduO gene an ATP:cob(I)alamin adenosyltransferase gene. J. Bacteriol. 183:2001;1577-1584.
20. Jomaa H., Wiesner J., Sanderbrand S., Altincicek B., Weidemeyer C., Hintz M., Turbachova I., Eberl M., Zeidler J., Lichtenthaler H.K., Soldati D., Beck E. Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. Science. 285:1999;1573-1576.
21. Kanehisa M., Goto S., Kawashima S., Nakaya A. The KEGG databases at GenomeNet. Nucleic Acids Res. 30:2002;42-46.
22. Karp P.D. A strategy for database interoperation. J. Comp. Biol. 2:1995;573-586.
23. Koonin, E.V., Galperin, M.Y., 2003. Sequence - Evolution - Function: Computational Approaches in Comparative Genomics. Kluwer Academic Publishers, Boston, MA. pp. 461.
24. Lo Conte L., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin A.G. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids. Res. 30:2002;264-267.
25. Marcotte E.M., Pellegrini M., Thompson M.J., Yeates T.O., Eisenberg D. Combined algorithm for genome-wide prediction of protein function. Nature. 402:1999a;83-86.
26. Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 285:1999b;751-753.
27. Morett E., Korbel J.O., Rajan E., Saab-Rincon G., Olvera L., Olvera M., Schmidt S., Snel B., Bork P. Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat. Biotechnol. 21:2003;790-795.
28. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Barrell D., Bateman A., Binns D., Biswas M., Bradley P., Bork P., Bucher P., Copley R.R., Courcelle E., Das U., Durbin R., Falquet L., Fleischmann W., Griffiths-Jones S., Haft D., Harte N., Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lopez R., Letunic I., Lonsdale D., Silventoinen V., Orchard S.E., Pagni M., Peyruc D., Ponting C.P., Selengut J.D., Servant F., Sigrist C.J., Vaughan R., Zdobnov E.M. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 31:2003;315-318.
29. Osterman A., Overbeek R. Missing genes in metabolic pathways: a comparative genomics approach. Curr. Opin. Chem. Biol. 7:2003;238-251.
30. Overbeek R., Fonstein M., D'Souza M., Pusch G.D., Maltsev N. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. U.S.A. 96:1999;2896-2901.
31. Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., Yeates T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. U.S.A. 96:1999;4285-4288.
32. Walhout A.J., Reboul J., Shtanko O., Bertin N., Vaglio P., Ge H., Lee H., Doucette-Stamm L., Gunsalus K.C., Schetter A.J., Morton D.G., Kemphues K.J., Reinke V., Kim S.K., Piano F., Vidal M. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr Biol. 12:2002;1952-1958.
33. Westbrook J., Feng Z., Chen L., Yang H., Berman H.M. The Protein Data Bank and structural genomics. Nucleic Acids Res. 31:2003;489-491.
34. Wu C.H., Xiao C., Hou Z., Huang H., Barker W.C. iProClass: an integrated, comprehensive and annotated protein classification database. Nucleic Acids Res. 29:2001;52-54.
35. Wu C.H., Huang H., Yeh L.-S., Barker W.C. Protein family classification and functional annotation. Comp. Biol. Chem. 27:2003a;37-47.
36. Wu C.H., Yeh L.-S., Huang H., Arminski L., Castro-Alvear J., Chen Y., Hu Z., Kourtesis P., Ledley R.S., Suzek B.E., Vinayaka C.R., Zhang J., Barker W.C. The Protein Information Resource. Nucleic Acids Res. 31:2003b;345-347.
37. Wu, C.H., Nikolskaya, A., Huang, H., Yeh, L.-.S., Natale, D., Vinayaka, C.R., Hu, Z., Mazumder, R., Kumar, S., Kourtesis, P., Ledley, R.S., Suzek, B.E., Arminski, L., Chen, Y., Zhang, J., Cardenas, J.L., Chung, S., Castro-Alvear, J., Dinkov, G., Barker, W.C., (2004). PIRSF family classification system at the Protein Information Resource. Nucleic Acids Res., 32, (in press).