The proteome: structure, function and evolution

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Keiran FlemingMichael J E Sternberg

Abstract

This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural hom...Continue Reading

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Citations

Mar 28, 2009·Briefings in Bioinformatics·Jeffrey Skolnick, Michal Brylinski
Nov 21, 2008·Journal of the Royal Society, Interface·Gabrielle A ReevesJanet M Thornton
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Aug 30, 2013·Asia-Pacific Journal of Public Health·Zhiguang ZhaoHe Wang

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