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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 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

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[1] Gupta, A. Gandhimathi, A. Sharma, P. and Jayaram, B. (2007) ParDOCK: An All Atom Energy Based Monte Carlo Docking Protocol for Protein-Ligand Complexes. Protein and Peptide Letters, Manuscript accepted

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