Hello, please help me with a docking problem in HEX 8.0. I try to dock ethidium bromide into the structure of a B-DNA DODECAMER (1BNA) and I hope to find an intercalation mode of binding as it is a known DNA intercalator but the docking simulation shows binding into the minor groove of DNA. After I download the pdb structure of DNA I remove the water molecules and save it as pdb format. I optimize the structure of Ethidium bromide in Avogadro 1.01 and then open the receptor (DNA) and the ligand (Ethidium Bromide) in HEX 8.0 and do the docking with the automatic settings (Correlation Type - Shape Only). Where am I wrong? Thank you for your time!
Why Don't you try AutoDock rather than Hex?
Use the following playlist for tutorial
https://www.youtube.com/playlist?list=PLFdE2bf3lv9w5LJwkZo4pM8relZWDb9X6
Dr. Rohan Meshram, I thought that HEX is preferred for DNA docking. I have just started working with HEX and I am still learning. Autodock I have used for docking small molecules into the active site of some enzymes. But I will try that, thank you! I haven't seen these tutorials up to now so thank you for that also!
Ian Hu, I also tought about that, but I saw some publications in which they represent an intercalating binding mode of some ligands by using HEX software. So I don't know...
Hi Theodora.
The PDB you are using has the nitrogenous bases very close together. You will hardly get intercalation by docking, just by molecular dynamics.
Try using PDB 1G3X. If not, possibly only molecular dynamics will solve your problem.
Read this article as a reference https://pubs.rsc.org/en/content/articlelanding/2021/NJ/D1NJ02105B
Hi Igor,
Thank you so much for the suggestion. I will look into that!
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