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Bioinformatics Advance Access published online on November 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti751
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 18, 2005
Accepted October 27, 2005

Article

SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles

Jan E. Gewehr 1* and Ralf Zimmer 1

1 Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University, Amalienstr. 17, D-80333 Munich, Germany

* To whom correspondence should be addressed.
Jan E. Gewehr, E-mail: jan.gewehr{at}bio.ifi.lmu.de


  Abstract

Motivation: The prediction of protein domains is a crucial task for functional classification, homology-based structure prediction, and structural genomics. In this paper, we present the SSEP-Domain protein domain prediction approach, which is based on the application of secondary structure element alignment and profile-profile alignment in combination with InterPro pattern searches. Secondary structure element alignment allows rapid screening for potential domain regions while profile-profile alignment provides us with the necessary specificity for selecting significant hits. The combination with InterPro patterns allows finding domain regions without solved structural templates if sequence family definitions exist.

Results: A preliminary version of SSEP-Domain was ranked among the top-performing domain prediction servers in the CASP 6 and CAFASP 4 experiments. Evaluation of the final version shows further improvement over these results together with a significant speed-up.

Availability: The server, supplementary information, and the detailed predictions are available at http://www.bio.ifi.lmu.de/SSEP/.


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