2023-02-07 Protein-ligand benchmarks meeting notes

Participants

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

Item	Presenter	Notes