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FEP tutorial for protein-protein binding #10

Closed kexul closed 3 years ago

kexul commented 3 years ago

Hi guys, thanks for your series of FEP tutorials, BioSimSpace is a powerful tool to assess the protein-small molecule ligand binding affinities. Recently, I'm trying to model protein-protein binding by free energy calculations, which were used to optimize antibody potency. After some search, I found there was no such information related to that topic in BioSimSpaces' materials. I would like to ask:

  1. Would that be feasible for the current version of BioSimSpace?
  2. If it's not feasible yet, would that capability be added in the future?

Thanks~

jmichel80 commented 3 years ago

Hi @kexul protein FEP would certainly be feasible with Gromacs has a back-end, but we do not support this feature at the moment. SOMD doesn't support this feature currently, and neither does the AMBER FEP implementation (I think). Eventually we plan to have a range of free energy protocols in BioSimSpace plugging in different backends but I don't think protein FEP will be implemented by us soon.

kexul commented 3 years ago

Get it! Thanks for the information.