The SUPERFAMILY database in 2007: Families and functions

Nucleic Acids Research

Volumn 35, Issue SUPPL. 1, 2007, Pages

  Wilson, Derek ^d   Madera, Martin ^a   Vogel, Christine ^b   Chothia, Cyrus ^d   Gough, Julian ^c  

^a University of California Santa Cruz   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c INSTITUT PASTEUR   (France)

^d MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; GENOME ANALYSIS; GENOMICS; HIDDEN MARKOV MODEL; INFORMATION PROCESSING; INTERNET; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; SUPERFAMILY DATABSE;

DATABASES, PROTEIN; GENOMICS; INTERNET; PROTEIN STRUCTURE, TERTIARY; PROTEINS; USER-COMPUTER INTERFACE;

EID: 33846044585     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl910     Document Type: Article

References (23)

1. Madera,M., Vogel,C., Kummerfeld,S.K., Chothia,C. and Gough,J. (2004) The superfamily database in 2004: Additions and improvements. Nucleic Acids Res., 32, D235-D239.
2. Andreeva,A., Howorth,D., Brenner,S.E., Hubbard,T.J., Chothia,C. and Murzin,A.G. (2004) Scop database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Res., 32, D226-D229.
3. Wu,C.H., Apweiler,R., Bairoch,A., Natale,D.A., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez,R. et al. (2006) The universal protein resource (uniprot): An expanding universe of protein information. Nucleic Acids Res., 34, D187-D191.
4. Deshpande,N., Addess,K.J., Bluhm,W.F., Merino-Ott,J.C., Townsend-Merino,W., Zhang,Q., Knezevich,C., Xie,L., Chen,L., Feng,Z. et al. (2005) The RCSB Protein Data Bank: A redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res., 33, D233-D237.
5. 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 proteins of known structure. J. Mol. Biol., 313, 903-919.
6. Eddy,S.R. (1998) Profile hidden markov models. Bioinfomatics, 14, 755-763.
7. Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
8. Madera,M. and Gough,J. (2002) A comparison of profile hidden markov model procedures for remote homology detection. Nucleic Acids Res., 30, 4321-4328.
9. Wistrand,M. and Sonnhammer,E.L. (2005) Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinformatics, 6, 99-109.
10. Altschul,S.F., Madden,T.L., Schäffer,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.
11. Gansner,E.R. and North,S.C. (1999) An open graph visualization system and its applications to software engineering. Softw. Pract. Exp., 30, 1203-1233.
12. Batada,N.N. (2004) CNplot: Visualizing pre-clustered networks. Bioinformatics, 20, 1455-1456.
13. Birney,E., Andrews,D., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cox,T., Cunningham,F., Curwen,V., Cutts,T. et al. (2006) Ensembl. 2006. Nucleic Acids Res., 34, D556-D561.
14. Finn,R.D., Mistry,J., Schuster-Böckler,B., Griffiths-Jones,S., Hotlich,V., Lassmann,T., Moxon,S., Marshall,M., Khanna,A., Durbin,R. et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
15. Gough,J. (2006) Genomic scale sub-family assignment of protein domains. Nucleic Acids Res., 34, 3625-3633.
16. Kummerfeld,S.K. and Teichmann,S.A. (2006) DBD: A transcription factor prediction database. Nucleic Acids Res., 34, D74-D81.
17. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genet., 25, 25-29.
18. Yeats,C., Maibaum,M., Marsden,R., Dibley,M., Lee,D., Addou,S. and Orengo,C.A. (2006) Gene3D: Modeling protein structure, function and evolution. Nucleic Acids Res., 34, D281-D284.
19. Tatusov,R.L., Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V., Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N. et al. (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics, 4, 41-55.
20. Mulder,N.J., Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Binns,D., Bradley,P., Bork,P., Bucher,P., Cerutti,L. et al. (2005) Interpro, progress and status in 2005. Nucleic Acids Res., 33, D201-D205.
21. Vogel,C., Berzuini,C., Bashton,M., Gough,J. and Teichmann,S.A. (2004) Supra-domains: Evolutionary units larger than single protein domains. J. Mol. Biol., 336, 809-823.
22. Vogel,C., Teichmann,S.A. and Pereira-Leal,J. (2005) The relationship between domain duplication and recombination. J. Mol. Biol., 346, 355-365.
23. Vogel,C. and Chothia,C. (2006) Protein family expansions and biological complexity. PLoS Comput. Biol., 2, e48.