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Nucleic Acids Research 2006 34(Web Server issue):W325-W329; doi:10.1093/nar/gkl211
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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

kinDOCK: a tool for comparative docking of protein kinase ligands

Laetitia Martin1,2,3, Vincent Catherinot1,2,3 and Gilles Labesse1,2,3,*

1 Atelier de Bio- et Chimie-Informatique Structurale, Centre de Biochimie Structurale CNRS UMR5048, Montpellier, France 2 INSERM U554 Montpellier France 3 Universités Montpellier I & Montpellier II 29, rue de Navacelles 34090 Montpellier Cedex, France

*To whom correspondence should be addressed. Tel: +33 04 67 41 77 12; Fax: +33 04 67 41 79 13; Email: labesse{at}cbs.cnrs.fr

Received February 14, 2006. Revised March 24, 2006. Accepted March 24, 2006.

KinDOCK is a new web server for the analysis of ATP-binding sites of protein kinases. This characterization is based on the docking of ligands already co-crystallized with other protein kinases. A structural library of protein kinase–ligand complexes has been extracted from the Protein Data Bank (PDB). This library can provide both potential ligands and their putative binding orientation for a given protein kinase. After protein–protein structural superposition, the ligands are transferred from the template complexes to the target protein kinase. The resulting complexes are evaluated using the program SCORE to compute a theoretical affinity. They can be dynamically visualized to allow a rapid mapping of important steric clashes and potential substitutions relevant for specificity and affinity. These characteristics allow a quick characterization of protein kinase active sites including conformation changes potentially required to accommodate particular ligands. Additionally, promising pharmacophores can be identified in the focussed library. These features will help to rationalize or optimize virtual screening (VS) on larger chemical compound libraries. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/kindock/.


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