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Bioinformatics Advance Access originally published online on November 2, 2005
Bioinformatics 2006 22(2):181-187; 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{at}oxfordjournals.org

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

Jan E. Gewehr * and Ralf Zimmer

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

*To whom correspondence should be addressed.

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 (SSEA) and profile–profile alignment (PPA) in combination with InterPro pattern searches. SSEA allows rapid screening for potential domain regions while PPA 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 is available at http://www.bio.ifi.lmu.de/SSEP/

Contact: jan.gewehr{at}bio.ifi.lmu.de

Supplementary information: The supplementary data are available at http://www.bio.ifi.lmu.de/SSEP/

Received on October 18, 2005; accepted on October 27, 2005

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