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Structure comparison and protein structure classifications

Part 3. Proteomics

3.6. Proteome Families

Specialist Review

  1. Oliver Redfern,
  2. Christopher Bennett,
  3. Christine Orengo

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g306214

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Redfern, O., Bennett, C. and Orengo, C. 2005. Structure comparison and protein structure classifications. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.6:82.

Author Information

  1. University College London, London, UK

Publication History

  1. Published Online: 15 APR 2005

Abstract

As genes duplicate and mutate over the course of evolution, their sequences can diverge beyond recognition. However, the three-dimensional structures of these homologous proteins often remain conserved. When the number of solved structures in the Protein Databank (PDB) rose significantly in the early 1990s, it became possible to group these evolutionary relatives into protein families. Over time, this has given rise to comprehensive hierarchical databases of protein structures, such as CATH and SCOP, which rely on a combination of manual expert classification and structural comparison methods. There are over 50 of the latter algorithms, ranging from secondary structure fold comparison methods (GRATH, SSM) to more computationally intensive fragment and residue-based approaches, such as DALI, CE, and SSAP. This chapter reviews the most popular methods and how they are combined with sequence comparison to recognize protein homologs. Many protein family databases (CATH, SCOP) focus on structural domains, rather than on whole polypeptide chains, so we examine approaches to automatic domain boundary assignment algorithms in parallel with the construction of protein structure classifications.

Keywords:

  • protein structure comparison;
  • protein family databases;
  • CATH;
  • SCOP;
  • HMM;
  • SSAP;
  • CE;
  • DALI;
  • HOMSTRAD;
  • CAMPASS