I got 5 conformations of ligands (from clustering histogram) in docking, which among the 5 should be taken for simulation....For eg; among the 5, the third and fourth poses appear entirely different in their disposition when analysed using autodock analyse option
You should go ahead with the confirmation with the highest binding energy (the one with lowest kI).
Thank you for the response.
I have 5 conformations in the cluster, with the highest binding energy (lowest Ki). My doubt is among these five poses/conformations, how to choose that pose for further simulation or can I choose any pose for that ?
Since am a beginner in this, hope you ll help me out.
First load all the conformations and then select only the conformation with highest energy. Then you'll have only that single conformation on your Autodock window. Next load the macromolecule and write the complex in. pdb or. pdbqt format as required.
Dear Rahul Narayanan kindly go through the insightful comments of @Martin Klvana in the following thread. This will really help you in understanding the concept and then choosing the best docking pose for MD. (https://www.researchgate.net/post/Criteria_for_choosing_best_docked_pose_and_its_validation)
Further, Docking score in terms of binding affinity can sometimes be misleading. In my experiences, I have seen ligands with relatively low docking scores showing better interactions with receptor molecule and vice versa. So it will be a crucial step in order to proceed with your experiment. Experimental information of your receptor like binding site or known inhibitor will surely help you making the final decision.
Wish you good luck.
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