References
The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genet 2000, 25: 25–29. 10.1038/75556
Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247: 536–540. 10.1006/jmbi.1995.0159
Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes San Diego, California: Academic Press; 1992.
Bairoch A: The ENZYME database in 2000. Nucleic Acids Res 2000, 28: 304–305. 10.1093/nar/28.1.304
Tramontano A: An account of the Seventh Meeting of the Worldwide Critical Assessment of Techniques for Protein Structure Prediction. Febs J 2007.
Janin J: Welcome to CAPRI: A Critical Assessment of PRedicted Interactions. Proteins: Structure, Function and Genetics 2002, 47: 257. 10.1002/prot.10111
Melvin I, Ie E, Kuang R, Weston J, Noble WS, Leslie C: SVM-fold: a tool for discriminative multi-class protein fold and superfamily recognition. BMC Bioinformatics 2007, 8(Suppl 4):S2. 10.1186/1471-2105-8-S4-S2
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 3389–3402. 10.1093/nar/25.17.3389
Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C: Profile-based String Kernels for Remote Homology Detection and Motif Extraction. Proceedings of the Computational Systems Bioinformatics Conference (IEEE CSB) 2004.
Audit B, Levy ED, Gilks WR, Goldovsky L, Ouzounis CA: CORRIE: enzyme sequence annotation with confidence estimates. BMC Bioinformatics 2007, 8(Suppl 4):S3. 10.1186/1471-2105-8-S4-S3
Levy ED, Ouzounis CA, Gilks WR, Audit B: Probabilistic annotation of protein sequences based on functional classifications. BMC Bioinformatics 2005, 6: 302. 10.1186/1471-2105-6-302
Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A: The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics 2007, 8(Suppl 4):S4. 10.1186/1471-2105-8-S4-S4
Marti-Renom MA, Ilyin VA, Sali A: DBAli: a database of protein structure alignments. Bioinformatics 2001, 17: 746–7. 10.1093/bioinformatics/17.8.746
Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, et al.: The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res 2005, 33: D247-D251. 10.1093/nar/gki024
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, et al.: New developments in the InterPro database. Nucleic Acids Res 2007, 35: D224-D228. 10.1093/nar/gkl841
Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, et al.: Pfam: clans, web tools and services. Nucleic Acids Res 2006, 34: D247-D251. 10.1093/nar/gkj149
Stuart AC, Ilyin VA, Sali A: LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics 2002, 18: 200–1. 10.1093/bioinformatics/18.1.200
Davis FP, Sali A: PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 2005, 21: 1901–7. 10.1093/bioinformatics/bti277
Henschel A, Winter C, Kim WK, Schroeder M: Using structural motif descriptors for sequence-based binding site prediction. BMC Bioinformatics 2007, 8(Suppl 4):S5. 10.1186/1471-2105-8-S4-S5
Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJ: The PROSITE database. Nucleic Acids Res 2006, 34: D227–30. 10.1093/nar/gkj063
Bairoch A: PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res 1991, 19(Suppl):2241–5.
Li J, Halgamuge SK, Kells CI, Tang S-L: Gene function prediction based on genomic context clustering and discriminative learning: An application to bacteriophages. BMC Bioinformatics 2007, 8(Suppl 4):S6. 10.1186/1471-2105-8-S4-S6
Cokus S, Mizutani S, Pellegrini M: An improved method for identifying functionally-linked proteins using phylogenetic profiles. BMC Bioinformatics 2007, 8(Suppl 4):S7. 10.1186/1471-2105-8-S4-S7
Chua HN, Sung W-K, Wong L: Using indirect protein interactions for the prediction of Gene Ontology functions. BMC Bioinformatics 2007, 8(Suppl 4):S8. 10.1186/1471-2105-8-S4-S8
Chua HN, Sung WK, Wong L: Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 2006, 22: 1623–30. 10.1093/bioinformatics/btl145
Xie L, Bourne PE: A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics 2007, 8(Suppl 4):S9. 10.1186/1471-2105-8-S4-S9
Yoon S, Ebert J, Chung E-Y, De Micheli G, Altman RB: Clustering protein environments for function prediction: finding PROSITE motifs in 3D. BMC Bioinformatics 2007, 8(Suppl 4):S10. 10.1186/1471-2105-8-S4-S10
Wei L, Altman RB: Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function. J Bioinform Comput Biol 2003, 1: 119–38. 10.1142/S0219720003000150
Wei L, Altman RB, Chang JT: Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences. Pac Symp Biocomput 1997, 465–76.
Wei L, Altman RB: Recognizing protein binding sites using statistical descriptions of their 3D environments. Pac Symp Biocomput 1998, 497–508.
Bagley SC, Wei L, Cheng C, Altman RB: Characterizing oriented protein structural sites using biochemical properties. Proc Int Conf Intell Syst Mol Biol 1995, 3: 12–20.
Bagley SC, Altman RB: Characterizing the microenvironment surrounding protein sites. Protein Sci 1995, 4: 622–35.
Soro S, Tramontano A: The prediction of protein function at CASP6. Proteins 2005, 61(Suppl 7):201–13. 10.1002/prot.20738