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Getting the most out of protein family classification resources

Part 3. Proteomics

3.6. Proteome Families

Basic Techniques and Approaches

  1. Nicola J. Mulder

Published Online: 15 JUL 2005

DOI: 10.1002/047001153X.g306411

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Mulder, N. J. 2005. Getting the most out of protein family classification resources. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.6:93.

Author Information

  1. European Bioinformatics Institute, Cambridge, UK

Publication History

  1. Published Online: 15 JUL 2005

Abstract

Protein family classification resources include the following protein signature and protein clustering databases: Pfam, PRINTS, PROSITE, ProDom, TIGRFAMs, SMART, PIR SuperFamily, SUPERFAMILY, and CluSTr. SCOP and CATH classify protein structures, and Merops, Transport Classification, and so on, are specialized protein family resources. All of them have their individual websites and databases available for searching, and are intuitive to use. Some of them are integrated into InterPro, which serves the data and software from a single source, and thus makes using the individual data and software quick and easy to access. All of them are represented in SRS (sequence retrieval system), which provides an interface for simple and complex queries and facilitates linking between results and new data. The resources are simple to use and include help pages for users.

Keywords:

  • InterPro;
  • protein family;
  • domain;
  • automatic annotation;
  • domain composition;
  • InterProScan;
  • functional classification