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Literature DB >> 22923291

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

Abstract

UNLABELLED: High-quality enzyme function annotation is essential for understanding the biochemistry, metabolism and disease processes of organisms. Previously, we developed a multi-component high-precision enzyme function predictor, EFICAz(2) (enzyme function inference by a combined approach). Here, we present an updated improved version, EFICAz(2.5), that is trained on a significantly larger data set of enzyme sequences and PROSITE patterns. We also present the results of the application of EFICAz(2.5) to the enzyme reannotation of 396 genomes cataloged in the ENSEMBL database. AVAILABILITY: The EFICAz(2.5) server and database is freely available with a use-friendly interface at http://cssb.biology.gatech.edu/EFICAz2.5.

Mesh：

Substances：
Enzymes
Proteome

Year: 2012 PMID： 22923291 PMCID： PMC3467752 DOI： 10.1093/bioinformatics/bts510

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

13 in total

1. Enzyme-specific profiles for genome annotation: PRIAM.

Authors: Clotilde Claudel-Renard; Claude Chevalet; Thomas Faraut; Daniel Kahn
Journal: Nucleic Acids Res Date: 2003-11-15 Impact factor: 16.971

2. High-quality protein knowledge resource: SWISS-PROT and TrEMBL.

Authors: Claire O'Donovan; Maria Jesus Martin; Alexandre Gattiker; Elisabeth Gasteiger; Amos Bairoch; Rolf Apweiler
Journal: Brief Bioinform Date: 2002-09 Impact factor: 11.622

3. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference.

Authors: Weidong Tian; Adrian K Arakaki; Jeffrey Skolnick
Journal: Nucleic Acids Res Date: 2004-12-01 Impact factor: 16.971

Review 4. Automated protein function prediction--the genomic challenge.

Authors: Iddo Friedberg
Journal: Brief Bioinform Date: 2006-05-23 Impact factor: 11.622

5. Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases.

Authors: Chenggang Yu; Nela Zavaljevski; Valmik Desai; Jaques Reifman
Journal: Proteins Date: 2009-02-01

6. PROSITE, a protein domain database for functional characterization and annotation.

Authors: Christian J A Sigrist; Lorenzo Cerutti; Edouard de Castro; Petra S Langendijk-Genevaux; Virginie Bulliard; Amos Bairoch; Nicolas Hulo
Journal: Nucleic Acids Res Date: 2009-10-25 Impact factor: 16.971

7. Ensembl 2011.

Authors: Paul Flicek; M Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Yuan Chen; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Leo Gordon; Maurice Hendrix; Thibaut Hourlier; Nathan Johnson; Andreas Kähäri; Damian Keefe; Stephen Keenan; Rhoda Kinsella; Felix Kokocinski; Eugene Kulesha; Pontus Larsson; Ian Longden; William McLaren; Bert Overduin; Bethan Pritchard; Harpreet Singh Riat; Daniel Rios; Graham R S Ritchie; Magali Ruffier; Michael Schuster; Daniel Sobral; Giulietta Spudich; Y Amy Tang; Stephen Trevanion; Jana Vandrovcova; Albert J Vilella; Simon White; Steven P Wilder; Amonida Zadissa; Jorge Zamora; Bronwen L Aken; Ewan Birney; Fiona Cunningham; Ian Dunham; Richard Durbin; Xosé M Fernández-Suarez; Javier Herrero; Tim J P Hubbard; Anne Parker; Glenn Proctor; Jan Vogel; Stephen M J Searle
Journal: Nucleic Acids Res Date: 2010-11-02 Impact factor: 16.971

8. UniProt Knowledgebase: a hub of integrated protein data.

Authors: Michele Magrane
Journal: Database (Oxford) Date: 2011-03-29 Impact factor: 3.451

9. EFICAz2: enzyme function inference by a combined approach enhanced by machine learning.

Authors: Adrian K Arakaki; Ying Huang; Jeffrey Skolnick
Journal: BMC Bioinformatics Date: 2009-04-13 Impact factor: 3.169

10. Identification of metabolites with anticancer properties by computational metabolomics.

Authors: Adrian K Arakaki; Roman Mezencev; Nathan J Bowen; Ying Huang; John F McDonald; Jeffrey Skolnick
Journal: Mol Cancer Date: 2008-06-17 Impact factor: 27.401

27 in total

1. The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone.

Authors: Daniel Barry Roche; Thomas Brüls
Journal: Protein Sci Date: 2015-01-28 Impact factor: 6.725

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

1. Enzyme-specific profiles for genome annotation: PRIAM.

2. High-quality protein knowledge resource: SWISS-PROT and TrEMBL.

3. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference.

Review 4. Automated protein function prediction--the genomic challenge.

5. Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases.

6. PROSITE, a protein domain database for functional characterization and annotation.

7. Ensembl 2011.

8. UniProt Knowledgebase: a hub of integrated protein data.

9. EFICAz2: enzyme function inference by a combined approach enhanced by machine learning.

10. Identification of metabolites with anticancer properties by computational metabolomics.

1. The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone.

2. Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers.

3. Transcriptomic Analyses Elucidate Adaptive Differences of Closely Related Strains of Pseudomonas aeruginosa in Fuel.

4. Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism.

5. Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis.

6. Synthetic Biology Meets Machine Learning.

7. BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation.

Review 8. Machine learning for enzyme engineering, selection and design.

9. Machine learning differentiates enzymatic and non-enzymatic metals in proteins.

10. Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis.