2023-02-07 Protein-ligand benchmarks meeting notes

Participants

Goals

• DD : sprint retrospective

  • Review Done cards

    • what went well?

    • what didn’t?

    • what do we need to improve our approach?

• DD : next sprint begins tomorrow, spans 2/8 - 2/20

  • architecture overview : https://drive.google.com/file/d/1ZA-zuqrhKSlYBEiAIqxwNaHXvgJdlOkT/view?usp=share_link

  • alchemiscale 0.1.0 milestone

  • coordination board : alchemiscale : Phase 1 - MVP

  • updates on In Review, In Progress, and Available cards

  • create/nominate new cards for inclusion in this sprint

  • will post on #free-energy-benchmarking when next sprint is finalized

• RG : ComponentMapping scenarios bake-off

  • Should game through a library of scenarios, including:

    • charge transformations (how are dummy atoms represented in mapping)?

    • protein mutations

    • protein mutations on a dimer, but mutating on one of the monomers

    • transformations on one ligand where multiple ligands present

    • covalent transformation of ligand and protein

    • moving a ligand from one place to another

  • RG : game out on current implementation

  • DD : game out on how this would work with protocols using only mappings, not refering to ChemicalSystem component keys

Discussion topics

Action items

Decisions