How do I compute the ligand binding site through PASS software?

08 August 2013 1 9K Report

Can anyone provide the full procedure for ligand binding site through PASS software?

Hello.

If you already have the ligand in the binding site, use EPOS_BP (http://gepard.bioinformatik.uni-saarland.de/software/epos-bp). First, it will map any cavities of your protein, drawing a map with a calculation of the pocket properties volume, polarity, and depth.

Then, you can overlap ligand and protein to EPOS_BP calculate the subcavities that the ligand occupies (PASS algorithm) and determines all sorts of properties. Check this paper: http://pubs.acs.org/doi/abs/10.1021/ci400195v.

Ricardo

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