I am doing molecular docking of the molecules that I synthesize and I am wondering how many poses would be necessary. I am doing this in maestro with glide and in the beginning by default I put 10 poses, but why not 50 poses. What would be the reason to get 50 poses instead of 10 or to get 100 poses instead of 50 ?
Hi Pablo Cavagnero
It probably mainly depends on the surface area of your substrate and/or how many ligand binding sites there are. Hopefully, literature can help you with this information. Either way, I suppose the aim is to obtain as many ligand conformations for each binding site. After generating a certain number of docked poses, you might notice that the ligand conformations and their binding energies start to appear similar. In my opinion, this is where you can stop generating more poses.
If I were you, I would read the literature first. If that does not provide me with sufficient information, I would take an approximate guess on the number of poses (preferably a high number) by looking at the surface area and electrostatics of the substrate and ligand, and also the time / resources required to perform this calculation.
All the best.
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