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Nucleic Acids Res. 2015 Jul 1;43(W1):W148-53. doi: 10.1093/nar/gkv488. Epub 2015 May 11.

CATH FunFHMMer web server: protein functional annotations using functional family assignments.

Author information

1
Institute of Structural and Molecular Biology, UCL, Darwin Building, Gower Street, WC1E 6BT, UK sayoni.das.12@ucl.ac.uk.
2
Institute of Structural and Molecular Biology, UCL, Darwin Building, Gower Street, WC1E 6BT, UK i.sillitoe@ucl.a.uk.
3
Institute of Structural and Molecular Biology, UCL, Darwin Building, Gower Street, WC1E 6BT, UK.
4
Department of Biochemical Engineering, UCL, Gower Street, WC1E 6BT, UK.
5
Institute of Structural and Molecular Biology, UCL, Darwin Building, Gower Street, WC1E 6BT, UK c.orengo@ucl.ac.uk.

Abstract

The widening function annotation gap in protein databases and the increasing number and diversity of the proteins being sequenced presents new challenges to protein function prediction methods. Multidomain proteins complicate the protein sequence-structure-function relationship further as new combinations of domains can expand the functional repertoire, creating new proteins and functions. Here, we present the FunFHMMer web server, which provides Gene Ontology (GO) annotations for query protein sequences based on the functional classification of the domain-based CATH-Gene3D resource. Our server also provides valuable information for the prediction of functional sites. The predictive power of FunFHMMer has been validated on a set of 95 proteins where FunFHMMer performs better than BLAST, Pfam and CDD. Recent validation by an independent international competition ranks FunFHMMer as one of the top function prediction methods in predicting GO annotations for both the Biological Process and Molecular Function Ontology. The FunFHMMer web server is available at http://www.cathdb.info/search/by_funfhmmer.

PMID:
25964299
PMCID:
PMC4489299
DOI:
10.1093/nar/gkv488
[Indexed for MEDLINE]
Free PMC Article

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