Dear colleagues, I have some experience with MD for studies of drug-target interactions, mainly NAMD and Amber. For quite some time, I wanted to try studying the binding/unbinding process of the drug to/from its target. I was thinking of using Steered MD, is it a good approach? I have seen some tutorials for SMD to “unbind” the ligand but none such tutorial to “bind” a potential ligand to its target. Is it even doable this way? Have you come across some tutorials for this?
What should I consider for such simulations, e.g. should the protein be restrained to limit its movement and inherently the SMD vector? should I use temp/pressure control?
Thank you for your responses.
SMD would be a good method to study ligand binding. Recently we have studied transfer of a ligand from a host to a target protein and substrate dissociation at different temperature using steered dynamics. Links of the articles are attached.
We have used the metadynamics module of Desmond. There is no need to restrain the protein or ligand; distance restrain between them should be enough.
Article Host assisted molecular recognition by human serum albumin: ...
Article Dynamical Flexibility Modulates Catalytic Activity of a Ther...
@Uttam Pal thank you for the answer, I will take a look at the provided article. I asked about the restrains, temperature, etc... because when I tried the SMD some time ago, my protein was moving around a lot, very fast and ligand was then at completely different position relative to protein after a few ps, I need to try it again though
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