2022-10-11 Protein-ligand benchmarks meeting notes

protein-ligand-benchmark

• IA: merged #52 on plb; now working on thrombin elimination, has low dynamic range

  • JC : thrombin should be okay?

  • MB : also have this reference for thrombin: https://www.sciencedirect.com/science/article/abs/pii/S0022283609005075?via%3Dihub

    • this features ITC data

    • JC : ITC data is fairly useless in terms of dynamic range; so agree that we can drop thrombin for now, then re-curate with KI data to give it better dynamic range

    • IA: I think thrombin is otherwise a great target; can we re-curate it quickly?

    • MB: I can recurate it quickly

  • JC: want to get ITC ligands and get KIs

  • MB : will prepare thrombin from the above

• JC: need a changelog; what is our plan?

  • IA: PLB#66

• IA: highest priority for me is plb#68,#69

• IP: There’s also issue #70

  • DD: I’d like to get rid of that.

  • IP, IA: No objections.

• IA: squashed rings (plb#72)

  • MB: don’t see this in Maestro; perhaps an export problem

  • IA: not a blocker to 0.3.0; many of these clashes will minimize out

• IA: concerns from OpenFE board

  • folks would like to be looped in; proposing that we cut this release as a beta release, give two weeks for feedback, then do full release

  • OpenFE is going to be working on to reproduce historical results; trying to find primary sources for previously-published work

    • JC: that is admirable, but may not be possible?

      • collecting old data is only needed to compare, yes?

• DD: IA and I will eliminate 0.3.0 remaining issues, aim to cut a beta release

  • meeting on Thursday power hour

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Nonequilibrium cycling

• IP : worked with DD previous week; identified issue where perses component assumes there is always both a solvent and complex phase in the same workflow

  • requires some refactoring of the perses components to accommodate

  • JC : need to make sure the atom mapping for complex and solvent phases are identical

    • DD: atom mappings are specified on creation of the network, not at protocol runtime, so that should address this
      
      

Protocol settings

• MH : everything outstanding now working; ready for review from OpenFE folks

  • IA : let’s make reviewing this the focus of Friday’s OpenFE power hour

  • MH : that works

• DD : are you planning to migrate openff-models to the openforcefield org?

  • MH : not yet; want to avoid users using it if they stumble upon it in openforcefield org