Nucleic Acids Research Advance Access originally published online on April 19, 2008
Nucleic Acids Research 2008 36(Web Server issue):W223-W228; doi:10.1093/nar/gkn187
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W223-W228
Published by Oxford University Press 2008
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.
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PharmaGist: a webserver for ligand-based pharmacophore detection
1School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, 2Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel and 3Basic Research Program, SAIC-Frederick, Center for Cancer Research, Nanobiology Program, NCI-Frederick, Bldg 469, Rm 151, Frederick, MD 21702, USA
*To whom correspondence should be addressed. Tel/Fax: +972 3 640 6476; Email: duhovka{at}tau.ac.il
Received February 4, 2008. Revised March 24, 2008. Accepted March 30, 2008.
Predicting molecular interactions is a major goal in rational drug design. Pharmacophore, which is the spatial arrangement of features that is essential for a molecule to interact with a specific target receptor, is an important model for achieving this goal. We present a freely available web server, named PharmaGist, for pharmacophore detection. The employed method is ligand based. Namely, it does not require the structure of the target receptor. Instead, the input is a set of structures of drug-like molecules that are known to bind to the receptor. The output consists of candidate pharmacophores that are computed by multiple flexible alignment of the input ligands. The method handles the flexibility of the input ligands explicitly and in deterministic manner within the alignment process. PharmaGist is also highly efficient, where a typical run with up to 32 drug-like molecules takes seconds to a few minutes on a stardard PC. Another important characteristic is the capability of detecting pharmacophores shared by different subsets of input molecules. This capability is a key advantage when the ligands belong to different binding modes or when the input contains outliers. The webserver has a user-friendly interface available at http://bioinfo3d.cs.tau.ac.il/PharmaGist.
The publisher or recipient acknowledges right of the U.S. Government to retain a nonexclusive, royalty-free license in and to any copyright covering the article.
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors
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