Closed pgrinaway closed 8 years ago
Ok, after a chat with @jchodera, we'll keep the above list except:
Sounds great. We should include another example that tests @juliebehr's MutationEngine
too. There are mutations of T4 lysozyme that modulate the ligand affinities: L99A binders, L99A nonbinders, L99A/M102Q binders, L99A/M102Q non-binders, and a number of additional mutants in this paper.
Going to close this, since this is mostly done.
This is what I am currently thinking--please let me know if you disagree.
perses
has these parts which need development:*
TopologyProposalEngine
- this already has an implemented base class and subclasses for small molecules. The small molecule bits need to be refactored for two reasons:tleap
. This is lower priority, since I think the priority is getting something that actually works. This also doesn't change the outward-facing API.GeometryEngine
- This is implemented, but needs a couple things, some of which are high priority:GeometryEngine
needs a suite of tests. This is very high priority and was the next thing I wanted to do.GeometryEngine
should use OpenMM to calculate potentials. The code for this is already started, but is in the unmerged closed PR. Now that we have a set goal, I can finish this. This is also very high priority.AlchemicalEliminationEngine
andNCMCEngine
- complete.Sampler
classes (even if only using simple algorithms) need to be written in order to actually do anything withperses
. This is high priority.So, my near-term plan of action was, in order:
GeometryEngine
stuff.TopologyProposalEngine
to correctly deal with multiple possible alignments.SAMSSampler
andExpandedEnsembleSampler
.SAMSSampler
.After (3), we should be able to do relative free energy calculations with SAMS, as well as design with a fixed bias. I think that should be the initial goal here.
Does this sound ok?