PharmaGist is a freely available web server for pharmacophore detection. The employed method is ligand based. 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. We compute candidate pharmacophores by multiple flexible alignments of the input ligands. The main innovation of this approach is that the flexibility of the input ligands is handled explicitly and in deterministic manner within the alignment process. The method is 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 of the method is the capability of detecting pharmacophores shared by different subsets of input molecules.
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Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ.
PharmaGist: a webserver for ligand-based pharmacophore detection.
Nucl. Acids Res. (2008) 36 (suppl 2): W223-W228.