EFICAz2.5: Application of a high-precision enzyme function predictor to 396 proteomes

Bioinformatics

Volumn 28, Issue 20, 2012, Pages 2687-2688

  Kumar, Narendra ^a   Skolnick, Jeffrey ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; PROTEOME;

ARTICLE; CHEMISTRY; CLASSIFICATION; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; GENOME; HUMAN; METABOLISM; MOLECULAR GENETICS; SEQUENCE ANALYSIS;

DATABASES, GENETIC; ENZYMES; GENOME; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEOME; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84870431146     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts510     Document Type: Article

References (14)

1. Arakaki, A.K. et al. (2009) EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. BMC Bioinformatics, 10, 107.
2. Arakaki, A.K. et al. (2008) Identification of metabolites with anticancer properties by computational metabolomics. Mol. Cancer, 7, 57.
3. Claudel-Renard, C. et al. (2003) Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res., 31, 6633-6639.
4. Flicek, P. et al. (2011) Ensembl 2011. Nucleic Acids Res., 39, D800-D806.
5. Friedberg, I. (2006) Automated protein function prediction-the genomic challenge. Brief. Bioinform., 7, 225-242.
6. Ginsburg, H. (2009) Caveat emptor: limitations of the automated reconstruction of metabolic pathways in Plasmodium. Trends Parasitol, 25, 37-43.
7. Magrane, M. and Consortium, U. (2011) UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford), 2011, bar009.
8. O'Donovan, C. et al. (2002) High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief. Bioinform., 3, 275-284.
9. Punta, M. et al. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
10. Quester, S. and Schomburg, D. (2011) EnzymeDetector: an integrated enzyme function prediction tool and database. BMC Bioinformatics, 12, 376.
11. Sigrist, CJ. et al. (2010) PROSITE, a protein domain database for functional characterization and annotatio. Nucleic Acids Res., 38, D161-D166.
12. Tian, W. et al. (2004) EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic Acids Res., 32, 6226-6239.
13. Webb, E. (1992) Enzyme Nomenclature 1992: Recommendations of the Nomenclature Committee o f the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification Of Enzymes. Published for the international union of Biochemistry and Molecular Biology by Academic Press, San Diego.
14. Yu, C. et al. (2009) Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases. Proteins, 74, 449-460.