2024-01-10 Mitchell/Wagner Check-in meeting notes

General updates

• JW –

  • MT offline this week

  • Thanks for raising issues and responses

  • Gave you a mention in all-hands for the CZI application

Trello

https://trello.com/b/dzvFZnv4/infrastructurePreview

Workshop prep

https://openforcefield.atlassian.net/wiki/spaces/COMMS/pages/2719055920

• Protein prep workshop

  • JW – Is PDB2PQR unambiguously good? Compared to PDBFixer/reduce/PROTOSS/etc?

    • JM – Uses ProPKA under the hood.

    • JW – That’s good, I’ve heard of that.

  • JW – Protein with heme?

  • JW – Will this run on colab? The notebook you have now is running on your beefy machine

    • JM – Should be fine on colab, the slow steps are CPU limited.

  • JM – Tried OpenFold, huge weights file that needs to be loaded, very involved. Most of the workshop complexity would end up being getting it installed/weights downloaded/inference to run.

  • JW – Would be good to have a way to help people understand WHEN our tools can be used. Like a green/yellow/red system, where we say “if your input has green characteristics, it’s fine. If it has yellow, then you may need to use other tools/open a text editor/cut out some things. If it’s red, then this isn’t suitable for our ecosystem.”

• SMIRNOFF workshop

  • JM – Looking at some good candidate systems. Like CRISPR inhibitor (protein+NA+ligand).

• Signups

  • JM – Draft form -

  • Dates?

    • Feb 20, 28, Mar 12 @ 3 PM Los Angeles/10 AM Canberra

    • Apr 10, 17, 24 @ 2 PM Berlin/1 PM London/8 AM New York

    • We will confirm times at our next check in

To dos

1. (high) Have draft notebooks for all 3 workshops that at least run for Jan 17

2. (high) Have google signup forms for workshops ready for Jan 17

3. (medium) Fix openff-docs CI/figure out what’s up with deployments

4. (medium) Fix openff-docs env cache issue

5. (low) Reach out to science team for additional vignette ideas

6. (low) Propagate PDB-bond loading options into nglview