[BiO BB] Energy function for active site

[Sourangshu Bhattacharya]

Dear Mr. Canales,
Thank you very much for the information and very sorry for replying so 
late.
Actually I wasn't looking for the packages but the explicit equations and 
constants that model the ligand-receptor interactions.
Moreover, I believe DOCK is not freely available for download.
Do you think, Hydrophobicity plays any role in such interactions ?

Please let me know about your opinion.
Thank you

Sourangshu Bhattacharya
ISI Kolkata.


On Thu, 22 May 2003, Mauricio Canales wrote:

> Hello Sourangshu Bhattacharya
> 
> Depends on the caracteristics of  the ligand. If  it is a peptide a pretty
> known package
> is DOCK http://www.cmpharm.ucsf.edu/kuntz/.
> I used GRAMM, http://reco3.ams.sunysb.edu/gramm/
> which was the best classified protein-protein docking procedure
> on CASP2 at the momment of the work. A model of amyloide peptide was docked
> onto acetylcholinesterase surface from Torpedo and it was experimentally
> tested.
> Energy functions are described in references at web pages. Normally
> they put more importance on nonbonded interactions: vanderwaals,
> electrostatics and h-bonds.
> I have not actualized later this topic so if you find other best procedures
> let me know it.
> 
> Mauricio
> 
> Center for Biotechnology
> UTFSM
> Valparaiso Chile
> Phone 56-32-654730
> Fax 56-32- 654783
> 
> 
> ----- Original Message -----
> From: "Sourangshu Bhattacharya" <mtc0119 at isical.ac.in>
> To: <bio_bulletin_board at bioinformatics.org>
> Sent: Wednesday, May 21, 2003 9:06 AM
> Subject: [BiO BB] Energy function for active site
> 
> 
> > Hi Everyone,
> > I am a newbie to this group. I dont know whether this is the right plaace
> > to ask such a question.
> >
> > Can anyone suggest me what are the avaiable energy functions for modelling
> > the interactions between a ligand and the protein atoms.
> >
> > Thank you very much.
> >
> > Sourangshu Bhattacharya
> > MTech Computer Science.
> >
> >
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> 
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-- 
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Sourangshu Bhattacharya
M.Tech. Computer Science,
Indian Statistical Institute,
Kolkata.
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