David L. Dotson

Awesome, thank you @jchodera! This is very helpful for us. Will work out our generalized approach for results using this as substrate.

Raw notes from story review, shared here for visibility: - the system shouldn't just be able to handle protein + ligand systems; it should support host+guest systems as well -...

Raw notes from story review, shared here for visibility: - drug discovery campaign support - wants to dock all proposed Enamine REALSpace compounds from Fragalysis using closest X-ray structure with...

Raw notes from story review, shared here for visibility: - our input network approach must be able to accommodate protein mutations for RBFE, not just ligand transformations - should allow...

Raw notes from story review, shared here for visibility: - a benchmarking campaign of its own, perhaps; doesn't necessarily need to be committed to by e.g. OpenFF or the Chodera...

Raw notes from story review, shared here for visibility: - want to be able to refine scoring methods for atom mappings in relative transformations, leading to more efficient transformation networks...

Raw notes from story review, shared here for visibility: - expanded ensemble approaches (single simulation REPEX) should be supported, not just non-equilibrium switching; also want plain old array of lambdas...

Raw notes from story review, shared here for visibility: - perhaps the most complex use case among the user stories; would generate graphs including both RBFE, ABFE transformations, operates in...

Raw notes from story review, shared here for visibility: - this story articulates OpenFF's direct need for the system; benchmarking feedback loop for biomolecule forcefield - transformations should be able...

Raw notes from story review, shared here for visibility: - need to be able to run equilibrium simulations, no alchemical transformations - other FFs besides OpenFF executable; engine doesn't matter,...