An overview of in silico protein function prediction

Archives of Microbiology

Volumn 192, Issue 3, 2010, Pages 151-155

  Sleator, Roy D ^a   Walsh, Paul ^a  

^a Munster Technological University   (Ireland)

Author keywords

Homology based transfer; Ontologies; Protein function; Sequence and structure Motifs

Indexed keywords

AMINO ACID SEQUENCE; COMPUTER MODEL; GENOMICS; METAGENOMICS; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN STRUCTURE; SHORT SURVEY; ANIMAL; CHEMISTRY; HUMAN; MOLECULAR GENETICS; REVIEW; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION;

PROTEIN;

ANIMALS; DATABASES, PROTEIN; HUMANS; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77950342398     PISSN: 03028933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00203-010-0549-9     Document Type: Short Survey

References (33)

1. Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
2. Ashburner M, Lewis S (2002) On ontologies for biologists: the Gene Ontology-untangling the web. Novartis Found Symp 247: 66-80; discussion 80-63, 84-90, 244-252
3. Attwood TK et al (2003) PRINTS and its automatic supplement, pre-PRINTS. Nucleic Acids Res 31:400-402
4. Bork P (2000) Powers and pitfalls in sequence analysis: the 70% hurdle. Genome Res 10:398-400
5. Breitkreutz BJ, Stark C, Tyers M (2003) The GRID: the general repository for interaction datasets. Genome Biol 4:R23
6. Di Gennaro JA et al (2001) Enhanced functional annotation of protein sequences via the use of structural descriptors. J Struct Biol 134:232-245
7. Eisenberg D, Marcotte EM, Xenarios I, Yeates TO (2000) Protein function in the post-genomic era. Nature 405:823-826
8. Enault F, Suhre K, Claverie JM (2005) Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis. BMC Bioinformatics 6:247
9. Friedberg I (2006) Automated protein function prediction-the genomic challenge. Brief Bioinform 7:225-242
10. Galperin MY, Walker DR, Koonin EV (1998) Analogous enzymes: independent inventions in enzyme evolution. Genome Res 8:779-790
11. Gibrat JF, Madej T, Bryant SH (1996) Surprising similarities in structure comparison. Curr Opin Struct Biol 6:377-385
12. Gilks WR, Audit B, de Angelis D, Tsoka S, Ouzounis CA (2005) Percolation of annotation errors through hierarchically structured protein sequence databases. Math Biosci 193:223-234
13. Godzik A, Jambon M, Friedberg I (2007) Computational protein function prediction: are we making progress? Cell Mol Life Sci 64:2505-2511
14. Goldsmith-Fischman S, Honig B (2003) Structural genomics: computational methods for structure analysis. Protein Sci 12:1813-1821
15. HenikoV JG, Greene EA, Pietrokovski S, HenikoV S (2000) Increased coverage of protein families with the blocks database servers. Nucleic Acids Res 28:228-230
16. Hulo N et al (2008) The 20 years of PROSITE. Nucleic Acids Res 36:D245-D249
17. JeVery CJ (2003) Moonlighting proteins: old proteins learning new tricks. Trends Genet 19:415-417
18. Jones S, Thornton JM (2004) Searching for functional sites in protein structures. Curr Opin Chem Biol 8:3-7
19. Laskowski RA, Watson JD, Thornton JM (2003) From protein structure to biochemical function? J Struct Funct Genomics 4:167-177
20. Lehne B, Schlitt T (2009) Protein-protein interaction databases: keeping up with growing interactomes. Hum Genomics 3:291-297
21. Losko S, Heumann K (2009) Semantic data integration and knowledge management to represent biological network associations. Methods Mol Biol 563:241-258
22. Rost B (2002) Enzyme function less conserved than anticipated. J Mol Biol 318:595-608
23. Rost B, Liu J, Nair R, Wrzeszczynski KO, Ofran Y (2003) Automatic prediction of protein function. Cell Mol Life Sci 60:2637-2650
24. Sharan R, Ulitsky I, Shamir R (2007) Network-based prediction of protein function. Mol Syst Biol 3:88
25. Sleator RD, Shortall C, Hill C (2008) Metagenomics. Lett Appl Microbiol 47:361-366
26. Smith CL, Goldsmith CA, Eppig JT (2005) The mammalian phenotype ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6:R7
27. Taubig H, Buchner A, Griebsch J (2006) PAST: fast structure-based searching in the PDB. Nucleic Acids Res 34:W20-W23
28. Todd AE, Orengo CA, Thornton JM (2001) Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 307:1113-1143
29. Walker MG, Volkmuth W, Sprinzak E, Hodgson D, Klingler T (1999) Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes. Genome Res 9:1198-1203
30. Wallace AC, Laskowski RA, Thornton JM (1996) Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci 5:1001-1013
31. Watson JD, Laskowski RA, Thornton JM (2005) Predicting protein function from sequence and structural data. Curr Opin Struct Biol 15:275-284
32. Ye Y, Godzik A (2004) FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res 32:W582-W585
33. Zhao XM, Chen L, Aihara K (2008) Protein function prediction with high-throughput data. Amino Acids 35:517-530