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. 2004 Jan 1;32(Database issue):D138-41.
doi: 10.1093/nar/gkh121.

The Pfam protein families database

Alex Bateman  1 , Lachlan Coin, Richard Durbin, Robert D Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L L Sonnhammer, David J Studholme, Corin Yeats, Sean R Eddy
Affiliations

The Pfam protein families database

Alex Bateman et al. Nucleic Acids Res. .

Abstract

Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations include modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in structure databases. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/).

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Figures

Figure 1
Figure 1
Comparison of Pfam, SCOP and CATH domain definitions for S-adenosylmethionine synthetase. The definitions of SCOP and Pfam are very similar, but rather different from the stricter structural definition of CATH. The definitions can be compared at the level of structure for each database. The two Rasmol windows on the right show the Pfam definition above the CATH definition.
Figure 2
Figure 2
Structure image coloured by Pfam domain, including a coloured domain key below. This structure shows the complex of P27, cyclin and CDK2. Clicking on the image links to the PDBsum resource (10).
See this image and copyright information in PMC

References

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