[Dock-fans] calculating binding sites volume overlap

[John J. Irwin]

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,
'jour', 'J Chem Inf Model.');> 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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>   
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