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Nucleic Acids Research Advance Access published online on May 8, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm301
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

ProMateus—an open research approach to protein-binding sites analysis

Hani Neuvirth1,2, Uri Heinemann1, David Birnbaum1, Naftali Tishby1 and Gideon Schreiber2,*

1School of Computer Science and Engineering, The Hebrew University Jerusalem, 91904 and 2Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel

*To whom correspondence should be addressed. Email: gidcon.Schreiber{at}weizmann.ac.il

Received January 29, 2007. Revised March 30, 2007. Accepted April 15, 2007.

The development of bioinformatic tools by individual labs results in the abundance of parallel programs for the same task. For example, identification of binding site regions between interacting proteins is done using: ProMate, WHISCY, PPI-Pred, PINUP and others. All servers first identify unique properties of binding sites and then incorporate them into a predictor. Obviously, the resulting prediction would improve if the most suitable parameters from each of those predictors would be incorporated into one server. However, because of the variation in methods and databases, this is currently not feasible. Here, the protein-binding site prediction server is extended into a general protein-binding sites research tool, ProMateus. This web tool, based on ProMate's infrastructure enables the easy exploration and incorporation of new features and databases by the user, providing an evaluation of the benefit of individual features and their combination within a set framework. This transforms the individual research into a community exercise, bringing out the best from all users for optimized predictions. The analysis is demonstrated on a database of protein protein and protein-DNA interactions. This approach is basically different from that used in generating meta-servers. The implications of the open-research approach are discussed. ProMateus is available at http://bip.weizmann.ac.il/promate.


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