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Functional prediction through phylogenetic inference and structural classification of proteins

Part 3. Proteomics

3.6. Proteome Families

Short Specialist Review

  1. Kimmen Sjölander,
  2. Chelsea Specht

Published Online: 15 JUL 2006

DOI: 10.1002/047001153X.g306320

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Sjölander, K. and Specht, C. 2006. Functional prediction through phylogenetic inference and structural classification of proteins. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.6.

Author Information

  1. University of California, Berkeley, CA, US

Publication History

  1. Published Online: 15 JUL 2006

Abstract

Computational prediction of gene function is an essential tool for modern biologists. The primary method of function prediction used today is based on homology, involving the transfer of annotation from the top hit in a database search to the gene of interest. However, homology-based methods of function prediction have been shown to be prone to systematic errors stemming from gene duplication, domain shuffling, and existing database errors. In recent years, methods of gene function prediction have focused on inclusion of information from evolutionary studies and structural analysis, and the success of these methods in inferring function from sequence data is very encouraging. In this paper, we present a perspective on the use of phylogenetic and structural analyses for improving the inference of protein function.

Keywords:

  • protein;
  • function prediction;
  • phylogeny;
  • structure;
  • structural classification;
  • phylogenomics