[Dock-fans] calculating binding sites volume overlap

[Paul Hawkins]

John,

Thanks for the hint to use OpenEye tools - the correct tool for this job is the shape toolkit or ROCS. RSR or RSCC require some way to calculate electron density, which is beyond most people in the modelling area.


Paul.
________________________________________
From: dock-fans-bounces at docking.org [dock-fans-bounces at docking.org] On Behalf Of John J. Irwin [jji at cgl.ucsf.edu]
Sent: Thursday, April 16, 2009 11:02 AM
To: Ben Keshet
Cc: dock-fans
Subject: Re: [Dock-fans] calculating binding sites volume overlap

Hi Ben
<http://xray.bmc.uu.se/usf/ligcom_man.html>
I saw this paper, but I don't know whether this idea is available is free, ready-to-go software: J Chem Inf Model.<javascript:AL_get(this,%20'jour',%20'J%20Chem%20Inf%20Model.');> 2008 Jul;48(7):1411-22. Epub 2008 Jul 4.
 An Alternative method for the evaluation of docking performance: RSR vs RMSD. by Yusuf D</sites/entrez?Db=pubmed&Cmd=Search&Term=%22Yusuf%20D%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus>, Davis AM</sites/entrez?Db=pubmed&Cmd=Search&Term=%22Davis%20AM%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus>, Kleywegt GJ</sites/entrez?Db=pubmed&Cmd=Search&Term=%22Kleywegt%20GJ%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus>, Schmitt S</sites/entrez?Db=pubmed&Cmd=Search&Term=%22Schmitt%20S%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus>.


There is also a program Ligcom that looks close-ish:
http://xray.bmc.uu.se/usf/ligcom_man.html. <http://xray.bmc.uu.se/usf/ligcom_man.html>

It also should be fairly straightforwared to do this with EON from Openeye.

Hope this is some use.

Good docking

John
UCSF DOCK Team


Ben Keshet wrote:

Hi Dock-fans,

I want to calculate the degree of volume overlap of two ligands docked
at close proximity (not at the same time). I thought of using sphgen to
generate the positive (inside surface) representation of the ligands as
a cluster of overlapping spheres. Then calculate the clusters volume
(say V1 and V2), and calculate the overlapping volume of V1 with V2,
which is the overlapping volume occupied by both ligands (separately,
not at the same time).

Does anyone know a tool that can do something like that (Dock, Chimera
or anything else)? Does anyone know if Mathematica is suitable for that?
The analytical solution becomes complicated when the number of spheres
increase, so I am trying to construct some numerical method to calculate
the overlapping volume (but I am not a programmer so it's becoming time
consuming). Any ideas are appreciated.

Thanks,
Ben Keshet
University of Maryland Baltimore County (UMBC)
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