Hello. I am new to molecular docking. I've been doing blind docking with a protein using Autodock and I got high reference RMSD values (around 100+) in my DLG files. What could be the problem? I've been searching for the reasons and found out one of the possible explanations (from FAQs section from Autodock website) to be the ligand input coordinates happen to be translated far from the receptor. So, could it be the explanation for my case? If yes, how can I improve from there?
I've attached two images to show the situation of my docking: (1) ligand and receptor input; (2) docked conformation (red indicates the ligand docked on the receptor).
Thank you.
Hi
Li Yuan Liew
Cluster RMSD is your actual RMSD value of ligand go to DLG file and again check.
Waseem Ahmad Ansari Thank you for your comment. I've got less than 2 angstrom for cluster RMSD. So, for my case, I will only need to refer to cluster RMSD, instead of reference RMSD?
Yes, because when we perform docking so docking generalize binding poses of top 10 in binding site during docking RMSD calculate respect to protein got it.
accually if you got a high RMSD more than 2,5 ,you should change your protein as this is only method for validation,please check your protein and try RMSD again
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