The prediction of protein function at CASP6

Proteins: Structure, Function and Genetics

Volumn 61, Issue SUPPL. 7, 2005, Pages 201-213

  Soro, Simonetta ^a   Tramontano, Anna ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Binding site; CASP6; Function prediction; GO categories

Indexed keywords

PROTEIN;

ANALYTIC METHOD; CASP6 SYSTEM; COMPUTER PREDICTION; COMPUTER SYSTEM; CONFERENCE PAPER; CONSENSUS; FUNCTIONAL MORPHOLOGY; NONHUMAN; PRIORITY JOURNAL; PROCESS DESIGN; PROTEIN FUNCTION; RELIABILITY;

ALGORITHMS; ANIMALS; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; COMPUTERS; DATABASES, PROTEIN; DIMERIZATION; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 30344440806     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20738     Document Type: Conference Paper

References (25)

1. Jones S, Thornton JM. Searching for functional sites in protein structures. Curr Opin Chem Biol 2004;8:3-7.
2. Gabaldon T, Huynen MA. Prediction of protein function and pathways in the genome era. Cell Mol Life Sci 2004;61:930-944.
3. Devos D, Valencia A. Practical limits of function prediction. Proteins 2000;41:98-107.
4. Rost B. Enzyme function less conserved than anticipated. J Mol Biol 2002;318:595-608.
5. Jeffery CJ. Moonlighting proteins: old proteins learning new tricks. Trends Genet 2003;19:415-417.
6. Jeffery CJ. Multifunctional proteins: examples of gene sharing. Ann Med 2003;35:28-35.
7. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R, Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004;32:D258-D261.
8. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003;31:3784-3788.
9. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. The Universal Protein Resource (UniProt). Nucleic Acids Res 2005;33:D154-D159.
10. Boeckmann B, Bairoch A, Apweiler R, Blatter M-C, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003;31: 365-370.
11. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH. InterPro, progress and status in 2005. Nucleic Acids Res 2005;33:D201-D205.
12. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM, DiCuccio M, Edgar R, Federhen S, Helmberg W, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pontius JU, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2005;33:D39-D45.
13. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2005;33:D54-D58.
14. Bateman A, Coin L, Durbin RD, Finn R, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, Studholme DJ, Yeats C, Eddy SR. The Pfam Protein Families Database. Nucleic Acids Res 2004;32:D138-D141.
15. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001;29:22-28.
16. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. The COG database: an updated version includes eukaryotes, BMC Bioinformatics 2003;4:41-54.
17. Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 2004;5:R7-R34.
18. Shin DH, Lou Y, Jancarik J, Yokota H, Kim R, Kim S-H. Crystal structure of Tm1457. Forthcoming.
19. Zemla A, Venclovas E, Moult J, Fidelis K. Processing and analysis of CASP3 protein structure predictions. Proteins 1999;S3:22-29.
20. Benach J, Lee I, Forouhar F, Kuzin AP, Keller JP, Itkin A, Xiao R, Acton T, Montelione GT, Hunt JF. X-ray structure of Yaeb from Haemophilus influenzae. Northeast Structural Genomics Research Consortium (Nesgc) Target Ir47. Forthcoming.
21. Joint Center for Structural Genomics: crystal structure of Pmba-related protein (Tm0727) from Thermotoga maritima at 1.95 A resolution. Forthcoming.
22. Kraiczy P, Hartmann K, Hellwage J, Skerka C, Kirschfink M, Brade V, Zipfel PF, Wallich R, Stevenson B. Immunological characterization of the complement regulator factor H-binding CRASP and Erp proteins of Borrelia burgdorferi. Int J Med Microbiol 2004;37:152-157.
23. Larson E, Reiter D, Young M, Lawrence CM. The structure of B116 from sulfolobus turreted icosahedral virus, a ubiquitous crenarchaeal viral protein. Forthcoming.
24. Das D, Oganesyan N, Yokota H, Pufan R, Kim R, Kim SH. Crystal structure of the conserved hypothetical protein Mpn330 (Gi: 1674200) from Mycoplasma pneumoniae. Proteins 2004;58:504-508.
25. Vincent JJ, Tai C-H, Sathyanarayana BK, Lee BK. Assessment of CASP6 predictions for new and nearly new fold targets. Proteins 2005;Suppl 7:67-83.