Hello,
I think the ccp4 program SC may help you. More info at
http://www.ccp4.ac.uk/ccp4/html/sc.html
Liz
On Monday 31 March 2008 14:08, Sangeetha Vedula wrote:
> Dear world,
>
> I am computing surface complementarity of one protein cavity with that of
> several ligands, for all of which I have X-ray crystal structures.
>
> I also need to compare the surface complementarities of each of the ligands
> to the protein with each other.
>
> Would anyone know of any program that I can use to accomplish this? Or, an
> algorithm that I can tweak to do the job? Something that determines how
> "parallel" the protein cavity and ligand surfaces are and assign a
> non-arbitrary score that I can use to compare across different ligands with
> the same (or similar) cavity, maybe? (The cavity does change slightly when
> different
> ligands bind).
>
> I would greatly appreciate any help or guidance.
>
> Thank you very much,
>
> Regards,
>
> Sangeetha Vedula.
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