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J Biol Chem. 2012 Jan 2;287(1):35-42. doi: 10.1074/jbc.R111.283408. Epub 2011 Nov 8.

Inference of functional properties from large-scale analysis of enzyme superfamilies.

Author information

1
Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, CA 94158-2330, USA.

Abstract

As increasingly large amounts of data from genome and other sequencing projects become available, new approaches are needed to determine the functions of the proteins these genes encode. We show how large-scale computational analysis can help to address this challenge by linking functional information to sequence and structural similarities using protein similarity networks. Network analyses using three functionally diverse enzyme superfamilies illustrate the use of these approaches for facile updating and comparison of available structures for a large superfamily, for creation of functional hypotheses for metagenomic sequences, and to summarize the limits of our functional knowledge about even well studied superfamilies.

PMID:
22069325
PMCID:
PMC3249087
DOI:
10.1074/jbc.R111.283408
[Indexed for MEDLINE]
Free PMC Article
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