Abstract:
: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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Schneidman-Duhovny D,Dror O,Inbar Y,Nussinov R,Wolfson HJdoi
10.1093/nar/gkn187subject
Has Abstractpub_date
2008-07-01 00:00:00pages
W223-8issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkn187journal_volume
36pub_type
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