Gene3D: Merging structure and function for a thousand genomes

Nucleic Acids Research

Volumn 38, Issue SUPPL.1, 2009, Pages

  Lees, Jonathan ^a   Yeats, Corin ^a   Redfern, Oliver ^a   Clegg, Andrew ^a   Orengo, Christine ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN DERIVATIVE;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; DNA POLYMORPHISM; GENE FUNCTION; GENE SEQUENCE; GENE STRUCTURE; GENOME; HIDDEN MARKOV MODEL; INTERNET; MULTIGENE FAMILY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; ALGORITHM; ANIMAL; ARCHAEAL GENOME; BACTERIAL GENOME; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC DATABASE; HUMAN; INFORMATION RETRIEVAL; METHODOLOGY; NUCLEIC ACID DATABASE; PROBABILITY; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; VIRUS GENOME;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOME, VIRAL; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MARKOV CHAINS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 75549086991     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp987     Document Type: Article

References (26)

1. Cuff, A.L., Sillitoe, I., Lewis, T., Redfern, O.C., Garratt, R., Thornton, J. and Orengo, C.A. (2009) The CATH classification revisited - architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res., 37, D310-D314.
2. UniProt Consortium. (2009) The Universal Protein Resource (UniProt). Nucleic Acids Res., 37, D169-D174.
3. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
4. Ward, J.J., Sodhi, J.S., McGuffin, L.J., Buxton, B.F. and Jones, D.T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol., 337, 635-645.
5. Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L. et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res., 37, D211-D215.
6. The Gene Ontology Consortium. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
7. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
8. Berman, H., Henrick, K., Nakamura, H. and Markley, J.L. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.
9. Karplus, K., Karchin, R., Draper, J., Casper, J., Mandel-Gutfreund, Y., Diekhans, M. and Hughey, R. (2003) Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction. Proteins: Struct. Funct. Gen., B, 491-496.
10. Sillitoe, I., Dibley, M., Bray, J., Addou, S. and Orengo, C. (2005) Assessing strategies for improved superfamily recognition. Protein Sci., 7, 1800-1810.
11. Hubbard, T.J., Aken, B.L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L. et al. (2009) Ensembl. Nucleic Acids Res., 37, D690-D697.
12. Ostergard, P.R.J. (2002) A fast algorithm for the maximum clique problem. Discr. Appl. Math., 120, 197-207.
13. Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Hotz, J.S., Ceric, H.R., Forslund, K., Eddy, S.R., Sonnhammer, E.L. and Bateman, A. (2008) The Pfam protein families database. Nucleic Acids Res., 36, D281-D288.
14. Kersey, P., Bower, L., Morris, L., Horne, A., Petryszak, R., Kanz, C., Kanapin, A., Das, U., Michoud, K., Phan, I. et al. (2005) Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res., 33, D297-D302.
15. Velankar, S., McNeil, P., Mittard-Runte, V., Suarez, A., Barrell, D., Apweiler, R. and Henrick, K. (2005) E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res., 33, D262-D265.
16. Jensen, L.J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. and Bork, P. (2008) eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res., 36, D250-D254.
17. Wilson, D., Pethica, R., Zhou, Y., Talbot, C., Vogel, C., Madera, M., Chothia, C. and Gough, J. (2009) SUPERFAMILY-sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res., 37, D380-D386.
18. Letunic, I., Doerks, T. and Bork, P. (2009) SMART 6: recent updates and new developments. Nucleic Acids Res., 37, D229-D232.
19. Krogh, A., Larsson, B., von Heijne, G. and Sonnhammer, E.L.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
20. Wootton, J.C. and Federhen, S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.
21. Lupas, A., Van Dyke, M. and Stock, J. (1991) Predicting coiled coils from protein sequences. Science, 252, 1162-1164.
22. Mi, H., Guo, N., Kejariwal, A. and Thomas, P.D. (2007) PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res., 35, D247-D252.
23. Chatr-aryamontri, A., Ceol, A., Palazzi, L.M., Nardelli, G., Schneider, M.V., Castagnoli, L. and Cesareni, G. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res., 35, D572-D574.
24. Kerrien, S., Alam-Faruque, Y., Aranda, B., Bancarz, I., Bridge, A., Derow, C., Dimmer, E., Feuermann, M., Friedrichsen, A., Huntley, R. et al. (2007) IntAct - open source resource for molecular interaction data. Nucleic Acids Res., 35, D561-D565.
25. Sayers, E.W., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S. et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37, D5-D15.
26. Rattei, T., Tischler, P., Arnold, R., Hamberger, F., Krebs, J., Krumsiek, J., Wachinger, B., Stümpflen, V. and Mewes, W. (2008) SIMAP - structuring the network of protein similarities. Nucleic Acids Res., 36, D289-D292.