Protarget: Automatic Prediction of Protein Structure Novelty

Publication Type

Journal Article

Publication Date

2005

Abstract

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.

Discipline

Bioinformatics | Computer Sciences

Publication

Nucleic Acids Research

Volume

33

Issue

Suppl. 2

First Page

W81

Last Page

W84

ISSN

0305-1048

Identifier

10.1093/nar/gki389

Publisher

Oxford

Additional URL

http://dx.doi.org/10.1093/nar/gki389

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