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Bioinformatics Advance Access published online on March 31, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti420
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 4, 2005
Revised March 18, 2005
Accepted March 30, 2005

Article

A comprehensive and non-redundant database of protein domain movements

Guoying Qi 1, Richard Lee 1, and Steven Hayward 2*

1 School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
2 School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK; School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK

* To whom correspondence should be addressed.
Steven Hayward, E-mail: sjh{at}cmp.uea.ac.uk


  Abstract

Motivation: The current DynDom database of protein domain motions is a user-created database that suffers from selectivity and redundancy. The aim of the analysis presented here was to overcome both these limitations and to produce both a comprehensive and non-redundant description of domain movements from structures stored in the current protein data bank.

Results: A multi-step procedure is applied that starts with grouping proteins in the structural databank into families based on sequence similarity. Multiple sequence alignment, conformational clustering, and a dimensional clustering method based on the Gram-Schmidt algorithm, are applied to members of each family to remove dynamic redundancy in their domain movements. Representative domain movements are described in terms of domains, hinge axes, and hinge-bending residues using the DynDom program. The results show that within an average family of 11.5 members there are on average only 1.31 different domain movements indicating a high redundancy in the movements these structures represent. This verifies earlier findings that domain movements are usually highly controlled. Despite the removal of this considerable redundancy the process has resulted in double the number of domain movements stored in the user-created database. The data is organised in a relational database with a web-interface.

Availability: The database can be browsed and searched at: http://www.cmp.uea.ac.uk/dyndom.


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