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Nucleic Acids Research 2005 33(Web Server Issue):W81-W84; doi:10.1093/nar/gki389
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Article

ProTarget: automatic prediction of protein structure novelty

Ori Sasson and Michal Linial1,*

School of Computer Science and Engineering, Institute of Life Sciences, Hebrew University of Jerusalem 91904 Israel 1Department of Biological Chemistry, Institute of Life Sciences, Hebrew University of Jerusalem 91904 Israel

*To whom correspondence should be addressed. Tel: +972 2 6585425; Fax: +972 2 6586448; Email: michall{at}cc.huji.ac.il

Received January 28, 2005. Revised March 10, 2005. Accepted March 10, 2005.

ProTarget is a Web-based tool for the automatic prediction of fold novelty. It offers the structural genomics community a method for target selection by providing an online analysis of any new or pre-existing sequence for its relationship to any previously solved three-dimensional structure. ProTarget takes as input an amino acid sequence. Regions of this sequence that exhibit high similarity to an existing PDB (Protein Data Bank) sequence are removed, leaving one or more subsequences. Each of these subsequences is then analyzed against a clustering of the protein space to determine the likelihood of its representing a new structural superfamily. This likelihood is derived from the distance in the clustering between the (sub)sequence and sequences that have known structures. The output of ProTarget is a graphical visualization of the protein of interest together with the likelihood that a protein sequence represents a novel structural superfamily. ProTarget is updated regularly and currently covers over 160 000 protein sequences from the SwissProt and PDB databases. ProTarget is available at http://www.protarget.cs.huji.ac.il.

Present address: Michal Linial, School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA


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