The 2006 automated function prediction meeting

BMC Bioinformatics

Volumn 8, Issue SUPPL. 4, 2007, Pages

  Rodrigues, Ana P C ^a   Grant, Barry J ^b   Godzik, Adam ^a,b   Friedberg, Iddo ^a  

^a BURNHAM INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED FUNCTIONS;

AMINO ACID SEQUENCE; AUTOMATION; BAYES THEOREM; BINDING SITE; COMPUTER PREDICTION; EDITORIAL; ENZYME ANALYSIS; FUNCTIONAL GENOMICS; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENE INTERACTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC DATABASE; LIGAND BINDING; MICROENVIRONMENT; PHYLOGENY; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RELIABILITY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURAL GENOMICS; STRUCTURAL HOMOLOGY; VALIDATION STUDY; BIOLOGY; CHEMISTRY; CONFERENCE PAPER;

PROTEIN;

COMPUTATIONAL BIOLOGY; PROTEINS;

EID: 45149115291     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S4-S1     Document Type: Editorial

References (33)

1. The Gene Ontology Consortium Gene Ontology: Tool for the unification of biology Nature Genet 2000, 25:25-29 10.1038/75556 10802651
2. 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 7723011
3. 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
4. Bairoch A The ENZYME database in 2000 Nucleic Acids Res 2000, 28:304-305 102465 10592255 10.1093/nar/28.1.304
5. Tramontano A An account of the Seventh Meeting of the Worldwide Critical Assessment of Techniques for Protein Structure Prediction Febs J 2007 17313483
6. Janin J Welcome to CAPRI: A Critical Assessment of PRedicted Interactions Proteins: Structure, Function and Genetics 2002, 47:257 10.1002/prot.10111
7. 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 1892081 17570145 10.1186/ 1471-2105-8-S4-S2
8. 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 146917 9254694 10.1093/nar/25.17.3389
9. 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
10. Audit B Levy ED Gilks WR Goldovsky L Ouzounis CA CORRIE: Enzyme sequence annotation with confidence estimates BMC Bioinformatics 2007, 8(Suppl 4):S3 1892082 17570146 10.1186/1471-2105-8-S4-S3
11. Levy ED Ouzounis CA Gilks WR Audit B Probabilistic annotation of protein sequences based on functional classifications BMC Bioinformatics 2005, 6:302 1361783 16354297 10.1186/1471-2105-6-302
12. 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 1892083 17570147 10.1186/1471-2105-8-S4-S4
13. 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 11524379
14. Pearl F Todd A Sillitoe I Dibley M Redfern O Lewis T Bennett C Marsden R Grant A Lee D 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 539978 15608188 10.1093/nar/gki024
15. Mulder NJ Apweiler R Attwood TK Bairoch A Bateman A Binns D Bork P Buillard V Cerutti L Copley R New developments in the InterPro database Nucleic Acids Res 2007, 35:D224-D228 10.1093/nar/gkl841 17202162 1899100
16. Finn RD Mistry J Schuster-Böckler B Griffiths-Jones S Hollich V Lassmann T Moxon S Marshall M Khanna A Durbin R Pfam: Clans, web tools and services Nucleic Acids Res 2006, 34:D247-D251 1347511 16381856 10.1093/nar/gkj149
17. 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 11836232
18. Davis FP Sali A PIBASE: A comprehensive database of structurally defined protein interfaces Bioinformatics 2005, 21:1901-7 10.1093/bioinformatics/ bti277 15657096
19. 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 1892084 17570148 10.1186/ 1471-2105-8-S4-S5
20. 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 1347426 16381852 10.1093/nar/gkj063
21. Bairoch A PROSITE: A dictionary of sites and patterns in proteins Nucleic Acids Res 1991, 19(Suppl):2241-5 331358 2041810
22. 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 1892085 17570149 10.1186/1471-2105-8-S4-S6
23. Cokus S Mizutani S Pellegrini M An improved method for identifying functionally-linked proteins using phylogenetic profiles BMC Bioinformatics 2007, 8(Suppl 4):S7 1892086 17570150 10.1186/ 1471-2105-8-S4-S7
24. 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 1892087 17570151 10.1186/1471-2105-8-S4-S8
25. 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 16632496
26. 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 1892088 17570152 10.1186/1471-2105-8-S4-S9
27. 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 1892080 17570144 10.1186/ 1471-2105-8-S4-S10
28. 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 15290784
29. 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 9390315
30. Wei L Altman RB Recognizing protein binding sites using statistical descriptions of their 3D environments Pac Symp Biocomput 1998:497-508 9697207
31. 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 7584427
32. Bagley SC Altman RB Characterizing the microenvironment surrounding protein sites Protein Sci 1995, 4:622-35 7613462
33. Soro S Tramontano A The prediction of protein function at CASP6 Proteins 2005, 61(Suppl 7):201-13 10.1002/prot.20738 16187363