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     DNA DOCKING
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DNA Ligand Docking is an all-atom energy based Monte Carlo DNA ligand docking, implemented in a fully automated, parallel processing mode which predicts the binding mode of the non-metallo ligand in the minor groove of DNA. The input is a DNA sequence and drug PDB file. The output will a docked structure alongwith the binding affinity of the docked structures.

'How to Use Tool'.

Step 1: Input DNA Sequence

Sequence      
Canonical DNA MD DNA
Step 2: Input Candidate Molecule & Charge [Sample File]:

Input PDB File      Net Ligand Charge +10 to -10


Step 3: Run Query

Job Id:       Please Specify Your Email Id :

 

References:

[1] S. A. Shaikh and B. Jayaram, "A Swift all-atom energy based computational protocol to predict DNA ligand binding affinity and ΔTm", J. Med. Chem., 2007, 50, 2240-2244.
http://pubs.acs.org/doi/abs/10.1021/jm060542c


[2] Gupta, A. Gandhimathi, P. Sharma, and B. Jayaram, "ParDOCK: An all atom energy based monte carlo docking protocol for protein-ligand complexes", Protein and Peptide Letters, 2007, 14, 632-646. 
http://www.ingentaconnect.com/content/ben/ppl/2007/00000014/00000007/art00003



For any exception/problem, kindly contact anjali@scfbio-iitd.res.in.


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