Hi, i am currently running an analysis for docking using acetylcholinesterase with a variety of novel compounds that I have synthesised. I am currently trying to decide which value for RMSD (cluster or reference) do I follow in order to get the best model or do I look at the free binding energy?
RMSD is not more than 2 A. By the way which software you have used.
Waseem Ahmad Ansari I am using PMV with Autodock4. Based on my results, the cluster RMSD was found to be smaller than that of my reference RMSD but I still do not know which one do I pay attention to
Mason Jarius Tangau
Hi
Go to dock dlg file and you will get RMSD table so in that table top rank cluster mentioned so which available on first rank with rmsd 0.0 you can choose for your screening.
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