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Is it possible to generate a structure-based pharmacophore model from the receptor binding site?

Yes. We recommend using the script E-Pharmacophores to guide the building of these types of receptor-based hypotheses. The script generates energetically optimized, structure-based pharmacophores, also known as e-pharmacophores, for use in rapid in silico screening. The method combines protein-ligand energetic terms computed by the Glide XP scoring function to rank the importance of pharmacophore features. The script is available from the Script Center, and is included in the software distribution from Suite 2011 on (Scripts → Docking Post-processing → E-Pharmacophores).

E-pharmacophores can be generated in cases where experimental information about ligand structure is unavailable, is not suitable for pharmacophore development (i.e., non druglike), or is at the site of a protein-protein interface; or where it is desirable to retrieve diverse compounds that are not biased by the cocrystallized ligand. However, it is possible that the best results will be obtained with an e-pharmacophore generated from docking a potent (or perhaps efficient) ligand for a given target.

There are two relevant papers describing the method and applications:

J. Chem. Inf. Model. 2009, 49, 2356 2368
J Comput Aided Mol Des (2009) 23:541554

Keywords: Structure-based pharmacophore, receptor-based pharmacophore, Phase, Glide XP, e-pharmacophores,

Related Articles:

#214: Can I create a pharmacophore hypothesis based only on my protein binding site, without having a native ligand?

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