Skip Navigation



Nucleic Acids Research Advance Access published online on April 19, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn187
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (3793K) Freely available
Right arrow Screen PDF (483K) Freely available
Right arrowOA All Versions of this Article:
36/suppl_2/W223    most recent
gkn187v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Schneidman-Duhovny, D.
Right arrow Articles by Wolfson, H. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Schneidman-Duhovny, D.
Right arrow Articles by Wolfson, H. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 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

PharmaGist: a webserver for ligand-based pharmacophore detection{dagger}

Dina Schneidman-Duhovny1,*, Oranit Dror1, Yuval Inbar1, Ruth Nussinov2,3 and Haim J. Wolfson1

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.

{dagger}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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
L. Li, K. Bum-Erdene, P. H. Baenziger, J. J. Rosen, J. R. Hemmert, J. A. Nellis, M. E. Pierce, and S. O. Meroueh
BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome
Nucleic Acids Res., November 18, 2009; (2009) gkp852v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. Sperandio, M. Petitjean, and P. Tuffery
wwLigCSRre: a 3D ligand-based server for hit identification and optimization
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W504 - W509.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.