| DH Attended+presented at German cheminformatics conference. Need to analyze Vytas’s data. Pharma benchmarking call. Working on writing benchmarking paper.
MT DD Led benchmarks meeting. Had previously decided that some datasets will be public (about 1400 compounds per partner). Each partner will have private, proprietary datasets Worked on software proposal, need to finish that up. Prepared some QCA datasets. One for Jessica Maat that I had promised a while ago. Another for John Chodera. Coordinated other QCA activity. DH – Action on dataset that Thomas Fox sent to Mobley? DD – Yes, I’ll redirect that to Gary Tresadern and myself, and have those added to public datasets. DH – I’ve looked at the compounds, it’s SMILES w/o hydrogens and w/o stereo DD – We’ll need better resolution on those compounds. I’ll follow up with TF and DM.
Need to figure out plans intelligent exploration subgroup – Looking for feedback on how scheduling/attendance will be MT – I think it should keep going in some capacity. Not sure about pacing, could solicit more feedback. DD – I’ll put out a poll for participants and decide on a path forward.
JW Worked on fixing Zenodo authorship – Webhooks are still tied to Chodera. Got login for info@openff and will move Zenodo hooks over that way. Contacted conda-forge folks on gitter. Probably made us look like clowns. Played with conf. gen CLI. Working on improving performance re: stereo and partial charges, output deduplication Some back-and-forth on issues and PRs. Started Toolkit Showcase example PR. TG discussion – Directions for authorship. Need to talk with him and Mobley about how to get on papers.
PB Worked on WBOs and fitting. Some progress on separating trends based on chemical series. Iterating on some sets – will do Trevor’s next (currently working on Lim+Mobley mols) Worked on preparing some datasets involving protomer/tautomer enumeration. JH is thinking about ligand expo set Talked with Hyesu about getting involved in QM benchmark, expect to hear from her this week. Q: How to filter benchmark molecules? Using RDKit fingerprint. I’d like to exclude benchmarking molecules from my testing set.
DH – Thinking about PLBenchmark repo. Looked at doing a release, I find it overwhelming to keep track of the data – Should it go in GH release assets? Git tree? Zenodo assets?. DH – Would like to be able to track the dataset changes between releases DH – Currently datasets are in the 100MB → 1 GB range DD – Would be good to make a policy document on this. (General) – Goals: (General) – Options Github release assets Does get a stable URL Doesn’t track changes
Zenodo datasets Does get a stable URL Doesn’t track changes
Github git tree Git LFS? Google drive link
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