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Nucleic Acids Research 2004 32(Web Server Issue):W532-W535; doi:10.1093/nar/gkh357
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices

Andrew E. Torda*, James B. Procter and Thomas Huber1

University of Hamburg, Zentrum für Bioinformatik, Bundesstrasse 43, D-20146 Hamburg, Germany and 1 Departments of Mathematics and Biochemistry, University of Queensland, Brisbane, QLD 4072, Australia

* To whom correspondence should be addressed. Tel: +49 40 42838 7331; Fax: +49 40 42833 7332; Email: torda{at}zbh.uni-hamburg.de

Received February 10, 2004; Revised and Accepted February 25, 2004

Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms. The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure. A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles.

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