{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T19:06:50Z","timestamp":1760728010553},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"S4","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,5]]},"DOI":"10.1186\/1471-2105-8-s4-s1","type":"journal-article","created":{"date-parts":[[2007,5,23]],"date-time":"2007-05-23T16:36:58Z","timestamp":1179938218000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["The 2006 Automated Function Prediction Meeting"],"prefix":"10.1186","volume":"8","author":[{"given":"Ana PC","family":"Rodrigues","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barry J","family":"Grant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam","family":"Godzik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iddo","family":"Friedberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,5,22]]},"reference":[{"key":"1904_CR1","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"The Gene Ontology Consortium","year":"2000","unstructured":"The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genet 2000, 25: 25\u201329. 10.1038\/75556","journal-title":"Nature Genet"},{"key":"1904_CR2","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1006\/jmbi.1995.0159","volume":"247","author":"AG Murzin","year":"1995","unstructured":"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\u2013540. 10.1006\/jmbi.1995.0159","journal-title":"J Mol Biol"},{"key":"1904_CR3","unstructured":"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."},{"key":"1904_CR4","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1093\/nar\/28.1.304","volume":"28","author":"A Bairoch","year":"2000","unstructured":"Bairoch A: The ENZYME database in 2000. Nucleic Acids Res 2000, 28: 304\u2013305. 10.1093\/nar\/28.1.304","journal-title":"Nucleic Acids Res"},{"key":"1904_CR5","volume-title":"Febs J","author":"A Tramontano","year":"2007","unstructured":"Tramontano A: An account of the Seventh Meeting of the Worldwide Critical Assessment of Techniques for Protein Structure Prediction. Febs J 2007."},{"key":"1904_CR6","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1002\/prot.10111","volume":"47","author":"J Janin","year":"2002","unstructured":"Janin J: Welcome to CAPRI: A Critical Assessment of PRedicted Interactions. Proteins: Structure, Function and Genetics 2002, 47: 257. 10.1002\/prot.10111","journal-title":"Proteins: Structure, Function and Genetics"},{"issue":"Suppl 4","key":"1904_CR7","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-8-S4-S2","volume":"8","author":"I Melvin","year":"2007","unstructured":"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","journal-title":"BMC Bioinformatics"},{"key":"1904_CR8","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Sch\u00e4ffer 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\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"key":"1904_CR9","volume-title":"Proceedings of the Computational Systems Bioinformatics Conference (IEEE CSB)","author":"R Kuang","year":"2004","unstructured":"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."},{"issue":"Suppl 4","key":"1904_CR10","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1186\/1471-2105-8-S4-S3","volume":"8","author":"B Audit","year":"2007","unstructured":"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","journal-title":"BMC Bioinformatics"},{"key":"1904_CR11","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1186\/1471-2105-6-302","volume":"6","author":"ED Levy","year":"2005","unstructured":"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","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 4","key":"1904_CR12","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/1471-2105-8-S4-S4","volume":"8","author":"MA Marti-Renom","year":"2007","unstructured":"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","journal-title":"BMC Bioinformatics"},{"key":"1904_CR13","doi-asserted-by":"publisher","first-page":"746","DOI":"10.1093\/bioinformatics\/17.8.746","volume":"17","author":"MA Marti-Renom","year":"2001","unstructured":"Marti-Renom MA, Ilyin VA, Sali A: DBAli: a database of protein structure alignments. Bioinformatics 2001, 17: 746\u20137. 10.1093\/bioinformatics\/17.8.746","journal-title":"Bioinformatics"},{"key":"1904_CR14","doi-asserted-by":"publisher","first-page":"D247","DOI":"10.1093\/nar\/gki024","volume":"33","author":"F Pearl","year":"2005","unstructured":"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","journal-title":"Nucleic Acids Res"},{"key":"1904_CR15","doi-asserted-by":"publisher","first-page":"D224","DOI":"10.1093\/nar\/gkl841","volume":"35","author":"NJ Mulder","year":"2007","unstructured":"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","journal-title":"Nucleic Acids Res"},{"key":"1904_CR16","doi-asserted-by":"publisher","first-page":"D247","DOI":"10.1093\/nar\/gkj149","volume":"34","author":"RD Finn","year":"2006","unstructured":"Finn RD, Mistry J, Schuster-B\u00f6ckler 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","journal-title":"Nucleic Acids Res"},{"key":"1904_CR17","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1093\/bioinformatics\/18.1.200","volume":"18","author":"AC Stuart","year":"2002","unstructured":"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\u20131. 10.1093\/bioinformatics\/18.1.200","journal-title":"Bioinformatics"},{"key":"1904_CR18","doi-asserted-by":"publisher","first-page":"1901","DOI":"10.1093\/bioinformatics\/bti277","volume":"21","author":"FP Davis","year":"2005","unstructured":"Davis FP, Sali A: PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 2005, 21: 1901\u20137. 10.1093\/bioinformatics\/bti277","journal-title":"Bioinformatics"},{"issue":"Suppl 4","key":"1904_CR19","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2105-8-S4-S5","volume":"8","author":"A Henschel","year":"2007","unstructured":"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","journal-title":"BMC Bioinformatics"},{"key":"1904_CR20","doi-asserted-by":"publisher","first-page":"D227","DOI":"10.1093\/nar\/gkj063","volume":"34","author":"N Hulo","year":"2006","unstructured":"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\u201330. 10.1093\/nar\/gkj063","journal-title":"Nucleic Acids Res"},{"issue":"Suppl","key":"1904_CR21","doi-asserted-by":"publisher","first-page":"2241","DOI":"10.1093\/nar\/19.suppl.2241","volume":"19","author":"A Bairoch","year":"1991","unstructured":"Bairoch A: PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res 1991, 19(Suppl):2241\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"Suppl 4","key":"1904_CR22","doi-asserted-by":"publisher","first-page":"S6","DOI":"10.1186\/1471-2105-8-S4-S6","volume":"8","author":"J Li","year":"2007","unstructured":"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","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 4","key":"1904_CR23","doi-asserted-by":"publisher","first-page":"S7","DOI":"10.1186\/1471-2105-8-S4-S7","volume":"8","author":"S Cokus","year":"2007","unstructured":"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","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 4","key":"1904_CR24","doi-asserted-by":"publisher","first-page":"S8","DOI":"10.1186\/1471-2105-8-S4-S8","volume":"8","author":"HN Chua","year":"2007","unstructured":"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","journal-title":"BMC Bioinformatics"},{"key":"1904_CR25","doi-asserted-by":"publisher","first-page":"1623","DOI":"10.1093\/bioinformatics\/btl145","volume":"22","author":"HN Chua","year":"2006","unstructured":"Chua HN, Sung WK, Wong L: Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 2006, 22: 1623\u201330. 10.1093\/bioinformatics\/btl145","journal-title":"Bioinformatics"},{"issue":"Suppl 4","key":"1904_CR26","doi-asserted-by":"publisher","first-page":"S9","DOI":"10.1186\/1471-2105-8-S4-S9","volume":"8","author":"L Xie","year":"2007","unstructured":"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","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 4","key":"1904_CR27","doi-asserted-by":"publisher","first-page":"S10","DOI":"10.1186\/1471-2105-8-S4-S10","volume":"8","author":"S Yoon","year":"2007","unstructured":"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","journal-title":"BMC Bioinformatics"},{"key":"1904_CR28","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1142\/S0219720003000150","volume":"1","author":"L Wei","year":"2003","unstructured":"Wei L, Altman RB: Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function. J Bioinform Comput Biol 2003, 1: 119\u201338. 10.1142\/S0219720003000150","journal-title":"J Bioinform Comput Biol"},{"key":"1904_CR29","first-page":"465","volume-title":"Pac Symp Biocomput","author":"L Wei","year":"1997","unstructured":"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\u201376."},{"key":"1904_CR30","first-page":"497","volume-title":"Pac Symp Biocomput","author":"L Wei","year":"1998","unstructured":"Wei L, Altman RB: Recognizing protein binding sites using statistical descriptions of their 3D environments. Pac Symp Biocomput 1998, 497\u2013508."},{"key":"1904_CR31","first-page":"12","volume":"3","author":"SC Bagley","year":"1995","unstructured":"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\u201320.","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"1904_CR32","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1002\/pro.5560040404","volume":"4","author":"SC Bagley","year":"1995","unstructured":"Bagley SC, Altman RB: Characterizing the microenvironment surrounding protein sites. Protein Sci 1995, 4: 622\u201335.","journal-title":"Protein Sci"},{"issue":"Suppl 7","key":"1904_CR33","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1002\/prot.20738","volume":"61","author":"S Soro","year":"2005","unstructured":"Soro S, Tramontano A: The prediction of protein function at CASP6. Proteins 2005, 61(Suppl 7):201\u201313. 10.1002\/prot.20738","journal-title":"Proteins"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-S4-S1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T21:19:13Z","timestamp":1630444753000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-S4-S1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,5]]},"references-count":33,"journal-issue":{"issue":"S4","published-print":{"date-parts":[[2007,5]]}},"alternative-id":["1904"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-s4-s1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,5]]},"assertion":[{"value":"22 May 2007","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S1"}}