GROMACS version: 2024.4
GROMACS modification: No
Context: I have experimental evidence that leads to believe my proteins of interest interact with a drug of interest. I want to produce a reasonable hypothesis, or set of hypotheses, about what regions of the protein(s) interact with the drug.
The CHARMM-GUI website has a Ligand Binding Site Finder & Refiner tool, which can produce simulation setup parameters for GROMACS, and the tool is asserted to produce biologically relevant predictions of the binding site, including its geometry.
I want to use the outputs of the LBS tool to first refine the predicted binding site, and then simulate the behavior once the drug of interest is introduced to the predicted binding site, with the idea being that this would produce sufficient evidence of interaction at that site to justify future experimental testing / validation.
I’ve run the CHARMM-GUI tool on the protein GMPR2, so I can attach the results of that if it is helpful.
My questions are essentially:
- Is it reasonable to use this strategy to produce predictions of a drug’s binding site?
- Are there existing guides on how to do something similar?
- How do I use the results of the LBS tool to achieve my goals?
I ask mostly in the hope that my overall strategy is similar enough to something already done that I can follow an example, rather than having to guess, as I have no expertise in this.
My thanks for any suggestions, references, advice, or other input.