Computational protocol: Interaction of 6 Mercaptopurine with Calf Thymus DNA – Deciphering the Binding Mode and Photoinduced DNA Damage

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Protocol publication

[…] HEX 6.3, a molecular graphics program, was used to study the 6MP-DNA interaction. Structure of the B–DNA dodecamer d(CGCGAATTCGCG)2 (PDB ID: 1BNA) was downloaded from the protein data bank (http://www.rcsb.org./pdb). Mol file of 6MP was obtained from http://www.drugbank.ca/drugs/DB01033 and further converted into PDB format using Avogadro’s 1.01. The Hex 6.3 performs docking using Spherical Polar Fourier Correlations. It necessitates the ligand and the receptor as input in PDB format. The parameters that were used for docking include: correlation type – shape only, FFT mode –3D, grid dimension –0.6, receptor range –180, ligand range –180, twist range –360, distance range –40. PyMol software was used for visualization of the docked pose. […]

Pipeline specifications

Software tools Avogadro, PyMOL
Databases DrugBank
Application Drug design
Organisms Bos taurus