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Briefings in Functional Genomics and Proteomics Advance Access published online on July 3, 2008
Briefings in Functional Genomics and Proteomics, doi:10.1093/bfgp/eln030
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© The Author 2008.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structure-based function prediction: approaches and applications

Pier Federico Gherardini and Manuela Helmer-Citterich

Corresponding author. Pier Federico Gherardini, Centre for Molecular Bioinformatics, Department of Biology, University of Tor Vergata, Rome, Italy. E-mail: pier.federico.gherardini{at}uniroma2.it

The ever increasing number of protein structures determined by structural genomic projects has spurred much interest in the development of methods for structure-based function prediction. Existing methods can be roughly classified in two groups: some use a comparative approach looking for the presence of structural motifs possibly associated with a known biochemical function. Other methods try to identify functional patches on the surface of a protein using only its physicochemical characteristics. This review will cover both kinds of approaches to structure-based function prediction as well as their use in real-world cases. The main issues and limitations in using protein structure to predict function will also be discussed. These are mainly: the assessment of the statistical significance of structural similarities and the extent to which these methods depend on the accuracy and availability of structural data.

Keywords: bioinformatics, function prediction, protein structure, structural comparison, active sites, structural genomics


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