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Nucleic Acids Research 2006 34(Web Server issue):W303-W309; doi:10.1093/nar/gkl344
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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

Protemot: prediction of protein binding sites with automatically extracted geometrical templates

Darby Tien-Hao Chang1,*, Yi-Zhong Weng1, Jung-Hsin Lin3, Ming-Jing Hwang4 and Yen-Jen Oyang1,2,*

1 Department of Computer Science and Information Engineering, National Taiwan University Taipei, 106, Taiwan, Republic of China 2 Graduate Institute of Networking and Multimedia, National Taiwan University Taipei 106, Taiwan, Republic of China 3 School of Pharmacy, National Taiwan University Taipei 106, Taiwan, Republic of China 4 Institute of Biomedical Sciences, Academia Sinica Taipei 115, Taiwan, Republic of China

*To whom correspondence should be addressed. Tel: +886-2-3366-4888 (ext. 431); Fax: +886-2-2368-8675; Email: darby{at}csie.ntu.edu.tw

Received February 14, 2006. Revised March 7, 2006. Accepted April 18, 2006.

Geometrical analysis of protein tertiary substructures has been an effective approach employed to predict protein binding sites. This article presents the Protemot web server that carries out prediction of protein binding sites based on the structural templates automatically extracted from the crystal structures of protein–ligand complexes in the PDB (Protein Data Bank). The automatic extraction mechanism is essential for creating and maintaining a comprehensive template library that timely accommodates to the new release of PDB as the number of entries continues to grow rapidly. The design of Protemot is also distinctive by the mechanism employed to expedite the analysis process that matches the tertiary substructures on the contour of the query protein with the templates in the library. This expediting mechanism is essential for providing reasonable response time to the user as the number of entries in the template library continues to grow rapidly due to rapid growth of the number of entries in PDB. This article also reports the experiments conducted to evaluate the prediction power delivered by the Protemot web server. Experimental results show that Protemot can deliver a superior prediction power than a web server based on a manually curated template library with insufficient quantity of entries. Availability: http://protemot.csie.ntu.edu.tw/step1.cgi http://bioinfo.mc.ntu.edu.tw/protemot/step1.cgi.

*Correspondence may also be addressed to Yen-Jen Oyang. Email: yjoyang{at}csie.ntu.edu.tw


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