[BiO BB] Energy function for active site

Mauricio Canales Mauricio.Canales at biotec.utfsm.cl
Thu May 22 07:03:25 EDT 2003

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
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.


Center for Biotechnology
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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