AMBER: Drug Leads interaction with ds and Triplex DNA

From: puneet kacker <>
Date: Wed, 24 Jan 2007 21:28:41 -0800 (PST)

Dear Amber Brothers
                   I am working with some noval DNA
binding Drug analogues to see their interactions with
ds and Triplex DNA. Some interesting things I want to
see with these are:

*Interactions Involve (Covalent and Non-covalent
between leads and DNA)
*Stability issue for the DNA(specificaly Triplex DNA)
*Place of Binding(Minor Vs Major)

Now my question is: If the Simulation is the right
choice then how I proceed? Is Docking necessry before
Note: Since Drug leads are novel in my case, they do't
have the crystal structure entry in RCSB-PDB.

Please help

Many Thanks

Puneet Kacker
Project Associate
Medicinal Chemistry Research Laboratory
Dr. B.R. Ambedkar Centre for Biomedical Research
University of Delhi-North Campus

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Received on Sun Jan 28 2007 - 06:07:13 PST
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