title: PharmaGist: a webserver for ligand-based pharmacophore detection.
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.
authors.affiliation: School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel. duhovka@tau.ac.il
authors.forename: Dina
authors.initials: D
authors.lastname: Schneidman-Duhovny
authors.forename: Oranit
authors.initials: O
authors.lastname: Dror
authors.forename: Yuval
authors.initials: Y
authors.lastname: Inbar
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
authors.forename: Haim J
authors.initials: HJ
authors.lastname: Wolfson
mesh_terms: D000465:Algorithms; D015195:Drug Design; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D004364:Pharmaceutical Preparations / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D004364:Pharmaceutical Preparations