Genomic scale sub-family assignment of protein domains

Nucleic Acids Research

Volumn 34, Issue 13, 2006, Pages 3625-3633

  Gough, Julian ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER ANALYSIS; CONTROLLED STUDY; GENE LIBRARY; GENOME ANALYSIS; GENOMICS; INFORMATION PROCESSING; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DOMAIN; BIOLOGY; CLASSIFICATION; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; PROTEIN TERTIARY STRUCTURE;

PROTEIN;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENOMICS; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 33746808240     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl484     Document Type: Article

References (36)

1. Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Cerutti,L., Corpet,F., Croning,M.D.R. et al. (2001) InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.
2. Gough,J., Karplus,K., Hughey,R. and Chothia,C. (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all protein of known structure. J. Mol. Biol., 313, 903-919.
3. Madera,M., Vogel,C., Kummerfeld,S., Chothia,C. and Gough,J. (2004) The superfamily database in 2004: Additions and improvements. Nucleic Acids Res., 32, 235-239.
4. Bateman,A., Birney,E., Durbin,R., Eddy,S.R., Howe,K.L. and Sonnhammer,E.L. (2000) The PFAM protein families database. Nucleic Acids Res., 28, 263-266.
5. 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.
6. 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.
7. Horn,F., Weare,J., Beukers,M.W., Horsch,S., Bairoch,A., Chen,W., Edvardsen,O., Campagne,F. and Vriend,G. (1998) Gpcrdb: An information system for g protein-coupled receptors. Nucleic Acids Res., 26, 277-81.
8. Vinogradov,S.N., Hoogewijs,D., Bailly,X., Arrendondo-Peter,R., Guertin,M., Gough,J., Dewilde,S., Moens,L. and Vanfleteren,J.R. (2005) Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. Proc. Natl Acad. Sci. USA, 102, 11385-11389.
9. Bashford,D., Chothia,C. and Lesk,A.M. (1987) Determinants of a protein fold. Unique features of the globin amino acid sequences. J. Mol. Biol., 196, 199-216.
10. Ravasi,T., Huber,T., Zavolan,M., Forrest,A., Gaasterland,T., Grimmond,S., Hume,D. and RIKEN GER Group,G.M. (2003) Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome Res., 13, 1430-1442.
11. Forrest,A.R., Ravasi,T., Taylor,D., Huber,T., Hume,D.A., Grimmond,S. and RIKEN GER Group,G.M. (2003) Phosphoregulators: Protein kinases and protein phosphatases of mouse. Genome Res., 13, 1443-1454.
12. Karchin,R., Karplus,K. and Haussler,D. (2002) Classifying G-protein coupled receptors with support vector machines. Bioinformatics, 18, 147-159.
13. Whelan,S., Debakker,P.I.W. and Goldman,N. (2003) Pandit: A database of protein and associated nucleotide domains with inferred trees. Bioinformatics, 19, 1556-1563.
14. Thomas,P.D., Campbell,M.J., Kejariwal,A., Mi,H., Karlak,B., Daverman,R., Diemer,K., Muruganujan,A. and Narechania,A. (2003) Panther: A library of protein families and subfamilies indexed by function. Genome Res., 13, 2129-2141.
15. Sjolander,K. (1998) Phylogenetic inference in protein superfamilies: analysis of SH2 domains. Proc. Int. Conf. Intell. Syst. Mol. Biol., 165-174.
16. Brown,D., Krishnamurthy,N., Dale,J.M., Christopher,W. and Sjolander,K. (2005) Subfamily HMMs in functional genomics. Pac. Symp. Biocomput. 2005, 322-333.
17. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
18. Karplus,K., Karchin,R., Shackelford,G. and Hughey,R. (2005) Calibrating E-values for hidden Markov models with reverse-sequence null models. Bioinformatics, 21, 4107-4115.
19. Park,J., Karplus,K., Barrett,C., Hughey,R., Haussler,D., Hubbard,T. and Chothia,C. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol., 284, 1201-1210.
20. Brenner,S.E., Chothia,C. and Hubbard,T.J. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci. USA, 95, 6073-6078.
21. Madera,M. and Gough,J. (2002) A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res., 30, 4321-4328.
22. Brenner,S.E., Koehl,P. and Levitt,M. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
23. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
24. Leinonen,R., Diez,F.G., Binns,D., Fleischmann,W., Lopez,R. and Apweiler,R. (2004) Uniprot archive. Bioinformatics, 20, 3236-3237.
25. Riley,M., Abe,T., Arnaud,M.B., Berlyn,M.K., Blattner,F.R., Chaudhuri,R.R., Glasner,J.D., Horiuchi,T., Keseler,I.M., Kosuge,T. et al. (2006) Escherichia coli K-12: A cooperatively developed annotation snapshot - 2005. Nucleic Acids Res., 34, 1-9.
26. Kummerfeld,S.K. and Teichmann,S.A. (2006) DBD: A transcription factor prediction database. Nucleic Acids Res., 34, D74-D81.
27. Podar,M., Eads,J.R. and Richardson,T.H. (2005) Evolution of a microbial nitrilase gene family: A comparative and environmental genomics study. BMC Evol. Biol., 5, 1-13.
28. Camon,E., Barrell,D., Brooksbank,C., Magrane,M. and Apweiler,R. (2003) The Gene Ontology Annotation (GOA) project: Application of GO in Swiss-Prot, Trembl and Interpro. Comp. Funct. Genom., 4, 71-74.
29. Camon,E., Barrell,D., Lee,V., Dimmer,E. and Apweiler,R. (2003) Gene Ontology annotation database - an integrated resource of GO annotations to Uniprot knowledgebase. In Silico Biol., 4, 2.
30. Bertone,P., Kluger,Y., Lan,N., Zheng,D., Christendat,D., Yee,A., Edwards,A., Arrowsmith,C., Montelione,G. and Gerstein,M. (2001) SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Res., 29, 2884-2998.
31. Brenner,S., Barken,D. and Levitt,M. (1999) The presage database for structural genomics. Nucleic Acids Res., 27, 251-253.
32. Moult,J., Pedersen,J.T., Judson,R. and Fidelis,K. (1995) A large-scale experiment to assess protein structure prediction methods. Proteins, 23, ii-v.
33. Koonin,E.V. (2005) Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet., 39, 309-338.
34. Vogel,C., Berzuini,C., Bashton,M., Gough,J. and Teichmann,S. (2004) Supra-domains - evolutionary units larger than single domains. J. Mol. Biol., 336, 809-823.
35. Gough,J. (2005) Convergent evolution of domain architectures (is rare). Bioinformatics, 21, 1464-1471.
36. Buchan,D.W., Shepherd,A.J., Lee,D., Pearl,F.M., Rison,S.C., Thornton,J.M. and Orengo,C.A. (2002) Gene3d: Structural assignment for whole genes and genomes using the cath domain structure database. Genome Res., 12, 503-514.