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Nucleic Acids Research 2006 34(Web Server issue):W164-W168; doi:10.1093/nar/gkl166
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines

Alessandro Vullo, Oscar Bortolami1, Gianluca Pollastri* and Silvio C. E. Tosatto1

School of Computer Science and Informatics, University College Dublin Ireland 1 Department of Biology and CRIBI Biotechnology Centre, University of Padova Italy

*To whom correspondence should be addressed. Tel: +353 1 716 2926; fax: +353 1 269 7262; Email: gianluca.pollastri{at}ucd.ie

Received February 13, 2006. Revised March 1, 2006. Accepted March 20, 2006.

Intrinsically disordered proteins have long stretches of their polypeptide chain, which do not adopt a single native structure composed of stable secondary and tertiary structure in the absence of binding partners. The prediction of intrinsically disordered regions in proteins from sequence is increasingly becoming of interest, as the presence of many such regions in the complete genome sequences are discovered and important functional roles are associated with them. We have developed a machine learning approach based on two support vector machines (SVM) to discriminate disordered regions from sequence. The SVM are trained and benchmarked on two sets, representing long and short disordered regions. A preliminary version of Spritz was shown to perform consistently well at the recent biannual CASP-6 experiment [Critical Assessment of Techniques for Protein Structure Prediction (CASP), 2004]. The fully developed Spritz method is freely available as a web server at http://distill.ucd.ie/spritz/ and http://protein.cribi.unipd.it/spritz/.


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