Assessment of predictions submitted for the CASP7 function prediction category

Proteins: Structure, Function and Genetics

Volumn 69, Issue SUPPL. 8, 2007, Pages 165-174

  López, Gonzalo ^a   Rojas, Ana ^a   Tress, Michael ^a   Valencia, Alfonso ^a  

^a Centro Nacional de Investigaciones Oncológicas   (Spain)

Author keywords

3D models; Binding sites; EC numbers; Function prediction; GO terms; Target structures

Indexed keywords

CASPASE 6; CASPASE 7;

BINDING SITE; CONFERENCE PAPER; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN TARGETING; SEQUENCE ANALYSIS;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 36748998785     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21651     Document Type: Conference Paper

References (28)

1. Friedberg I, Harder T, Godzik A. JAFA: a protein function annotation meta-server. Nucleic Acids Res 2006;34:W379-W381.
2. Hawkins T, Luban S, Kihara D. Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci 2006;15:1550-1556.
3. Laskowski RA, Watson JD, Thornton JM. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 2005;33:W89-W93.
4. Pazos F, Bang J-W. Computational prediction of functionally important regions in proteins. Curr Bioinform 2006;1:15-23.
5. Devos D, Valencia A. Practical limits of function prediction. Proteins 2000;41:98-107.
6. Todd AE, Orengo CA, Thornton JM. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 2001; 307:1113-1143.
7. Soro S, Tramontano A. The prediction of protein function at CASP6. Proteins 2005;61:201-213.
8. Kopp J, Schwede T. The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models Nucleic Acids Res 2004;32:D230-D234.
9. Castrignano T, De Meo PD, Cozzetto D, Talamo IG, Tramontano A. The PMDB protein model database. Nucleic Acids Res 2006;34:D306-D309.
10. Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 2006;34:D291-D295.
11. IUBMB. Enzyme Nomenclature. New York: Academic Press; 1992.
12. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 2000;25:25-29.
13. Altschul SF, Madden TL, Schaffer 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.
14. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
15. Clarke ND, Ezkurdia I, Kopp J, Read R, Schwede T, Tress ML. Domain definition and target classification for CASP7. Proteins, this issue.
16. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Natale DA, O'Donovan C, Redaschi N, Yeh LS. The universal protein resource (UniProt). Nucleic Acids Res 2005;33:D154-D159.
17. Lopez G, Valencia A, Tress ML. FireDB - a database of functionally important residues from proteins of known structure. Nucleic Acids Res 2007;35:D219-D223.
18. Zemla A. LGA - a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003;31:3370-3374.
19. Lopez G, Valencia A, Tress ML. firestar - prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res 2007;35: Web server issue, in press.
20. Tress ML, Grana O, Valencia A. SQUARE-determining reliable regions in sequence alignments. Bioinformatics 2004;20:974-975.
21. Michalsky E, Dunkel M, Goede A, Preissner R. SuperLigands - a database of ligand structures derived from the protein data bank. BMC Bioinform 2005;6:122.
22. Mitchell JBO. The relationship between the sequence identities of slpha helical proteins in the PDB and the molecular similarities of their ligands. J Chem Inf Comput Sci 2001;41:1617-1622.
23. Pellegrini-Calace M, Soro S, Tramontano A. Revisiting the prediction of protein function at CASP6. FEBS J 2006;273:2977-2983.
24. Janin J, Henrick K, Moult J, Ten Eyck L, Sternberg MJE, Vajda S, Vakser I, Wodak SJ. CAPRI: A Critical assessment of predicted interactions. Proteins 2003;52:2-9.
25. Friedberg I, Jambon M, Godzik A. New avenues in protein function prediction. Protein Sci 2006;15:1527-1529.
26. Hirschman L, Yeh A, Blaschke C, Valencia A. Overview of BioCreA-tIvE: critical assessment of information extraction for biology. BMC Bioinform 2005;6:S1.
27. In-silico prediction of gene function. Ref. U.E.: LSHG-CT-2004-503567.
28. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-108.