AMBER Archive (2007)

Subject: AMBER: Drug Leads interaction with ds and Triplex DNA

From: puneet kacker (puneet_bioinfo_at_yahoo.com)
Date: Wed Jan 24 2007 - 23:28:41 CST


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
simulation?
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
Delhi
INDIA

 
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