PharmaGist: a webserver for ligand-based pharmacophore detection

By Dina Schneidman-Duhovny, Oranit Dror, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson. 2008

264 citations recorded by the source corpus.

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.

Subfields: Computational Theory and Mathematics, Radiology, Nuclear Medicine and Imaging, Spectroscopy, Computational Chemistry & Drug Discovery

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Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, background): “Academic Hiphop [141] PharmaGist [154,155] HypoGen [141] ALADDIN [156] HypoRefine [141] RAPID [157] GASP [142,143] DANTE [158] DiscoTech [143,144] APOLLO [159] GALAHAD [143,145] CLEW [160] LigandScout [146,147] MPHIL [161] MOE [148,149] GAMMA [162] PHASE [150,151] SCAMPI [163] XED [152,153] Apex-3D…”
PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database (2017, background): “PharmaGist (8) is a free web server that can identify a consensus pharmacophore of a set of ligands in a few minutes.”
Pharmit: interactive exploration of chemical space (2016, methodology): “Al-ternatively, a pharmacophore query can be initialized using pharmacophore files in MOE (18), LigBuilder (19), Ligand-Scout (20), PharmaGist (21) or Pharmer (22) query formats.”
ZINCPharmer: pharmacophore search of the ZINC database (2012, background): “Alternatively, if there are many known binders then a consensus pharmacophore can be elucidated (1,4) using software such as Chemical Computing Group’s MOE (http://www.chemcomp.com/), Inte:Ligand’s LigandScout (http://www.inteligand.com/), or PharmaGist (5) and the result can be imported into ZINCPh”