Page Comparison

Participants

• David Dotson

• Richard Gowers

• David W.H. Swenson

• Irfan Alibay

• Iván Pulido

• Jenke Scheen

• John Chodera

• Levi Naden

• Meghan Osato

• Mike Henry

• Richard Gowers

• Jeffrey Wagner

Recording: https://drive.google.com/file/d/10ESg89Tt2xj5GkvqwsT2hM1BpA8YEGAu/view?usp=share_link

Goals

• DD : sprint retrospective

  • Review Done cards

    • what went well?

    • what didn’t?

    • what do we need to improve our approach?

• DD : alchemiscale 0.1.0 release imminent

  • architecture overview : https://drive.google.com/file/d/1ZA-zuqrhKSlYBEiAIqxwNaHXvgJdlOkT/view?usp=share_link

  • alchemiscale 0.1.0 milestone

    • Github link macro
      link https://github.com/openforcefield/alchemiscale/milestone/3

  • coordination board : alchemiscale : Phase 1 - MVP

  • updates on In Review, In Progress, and Available cards

  • No new sprint this week; will re-tool board for Phase 2 - User Feedback and Documentation

• IA : protein-ligand-benchmark : establish new working group, or use this one?

  • potential new participants

Discussion topics

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Notes
DD : sprint retrospective Review Done cards what went well? what didn’t? what do we need to improve our approach? DD – We now have everything merged for release 0.1. Big thanks to HMO for getting things in place. DD – Alchemiscale 102 – HMO set up a mechanism to rerun tasks that are inactive. DD – Gufe 148 – Needed different patterns in executedag that we needed. RG finished this and merged a few hours ago. RG – This was largely held up by a docstring formatting issue. DD – When will this be in a release? RG – By the end of the week. DD – Alchemiscale 150 – Pulled in tests for the above.
DD : alchemiscale 0.1.0 release imminent architecture overview : https://drive.google.com/file/d/1ZA-zuqrhKSlYBEiAIqxwNaHXvgJdlOkT/view?usp=share_link alchemiscale 0.1.0 milestone Github link macro link https://github.com/openforcefield/alchemiscale/milestone/3 coordination board : alchemiscale : Phase 1 - MVP updates on In Review, In Progress, and Available cards DD – Alchemiscale 112 – Some final prerelease changes. Would love a review. MH – I can review this. DD – Thanks, I’ll also ping HMO and take whoever reviews first. No new sprint this week; will re-tool board for Phase 2 - User Feedback and Documentation JW – openff-toolkit will have support for multi-component PDBs very soon (0.13 or 0.12.1); in the undetermined future, will also support custom substructures, which would open the door for support of other biopolymers, for example JC – we are actively working on RNA FFs, so definitely interested in this; espaloma FF JW – won’t have resources to pour into development of an RNA FF for this year ourselves RG – we can currently do this using the pdbinf tool; we go straight from RDKit → OpenMM currently JC – would avoid relying directly on OpenMM Topology long-term; the OpenFF Topology would be the better path long-term JW – OpenFE can load from correctly-named residues quickly; OpenFF approach will almost always be slower due to its element graph matching; using RG – Our philosphy is that we should always read well-formatted PDB files, with correctly named residues JC – The chemical component dictionary won’t have everything that could possibly be part of a protein. RG – Users could augment the CCD with their new residues JW – This wouldn’t work for polymer people and materials scientists (and we need to keep the door open for them) MH – Yeah, coming from the non-biopolymer world, I’ve seen people use workflows that required atom names and just get really put off by hacking in solutions. RG – Ok, well generally we’re sticking with residue name matching and we’ll need to load up multi-component rdmols into a Topology. JW – Sounds good, I can give tips on how to do this loaidng quickly (I’ve just been dealing with this) In review DD – Perses 1066 - IP how’s this going/ IP – I need to schedule meeting with JC and DD about this. DD – I’m happy to help get you up to date on the changes in gufe/other underlying stuff IA – PLB 83 – Working on this, we still want to do comparison testing to perses. DD – Last PR going into alchemiscale 0.1 - … MH or HMO will do this JC – – perses 1128 – Made progress. There’s some problem with atom mapping now. DD – Are they reversed? JC – Maybe JW – We updated molecule.remap to update the remapped atom's maps - So if a molecule originally contained atom_map={1:2}, and it’s remapped with a mapping containing {1:10}, then the final molecules will contain atom_map={10:2} JC – Interesting, I’ll check into that. JC – I’ll aim to ahve this done by Thursday, otherwise will hand off to IP/MH DD – Examplenotebooks 36 Rg – Waiting on the release we’re going ti amke, of gufe DD – Can I take on some of this? RG – Nope,we’re good
IA : protein-ligand-benchmark : establish new working group, or use this one? IA – potential new participants – Folks outside this working group want to contribute. Particularly MAria at OE want to help curate and contribute GPCR data. Also questions about maintenance - There’s a question from exscientia - Who are the responsible people for this? JC – Great question, we should get a group together to run this, potentially adjacent to this meeting. Could be good to start by looking into replacing schrodinger prep. So let’s convene a call. On our end, we could contribute folks to support this. I suppose there’s also interest from OFE. IA – I’ll check with our board. need a starting document to identify the working group; get commitments of resourcing from participants DD – Does it make sense to require that if folks want to be in the working group, they’ll also contribute resources? JC – Yes, very much so. There could still be advisory folks but most of the meetings would be among the actual contributors. JC – Any volunteers? IA – I couldn’t dedicate leadership-level energy for at least 6 months. Could open up invites on slack. JC – Agree that opening invites is a good idea - Is there someone who could lead meeting organization/scheduling? IP – I can do that. JC – Cool - That would be great. Make it clear that we’re looking for people who can do at least 2 hours a week helping do maintenance and handling requests. IP – Should I make these posts on free-energy-benchmarks? DD – Yes, I think so. It’ll be good to make sure the benchmarking paper authors give some sort of response. JS – IP, I can help lighten the load if needed. MH – Re: protein-prep tools - We’re taking about OE and Schrodinger - Are there open source tools we could use? JC – There’s basically nothing. I was hoping that ML could really assist here but that hasn’t turned out to be the case. At least OE Spruce is free for academics. DD – I wonder if OpenFold would be in a good spot to help with this. JC – That would make a lot of sense. OR the rosetta folks may be able to help as well IA – We’ve joked about OpenPrep before, but I think our partners would really be interested in this. Should we look down this avenue? JC – Yes IA – … MH – Yeah, the companies supporting OpenFE would very likely all be interested in this. DD – Agree, good opportunities for synergy here. MH – Could pitch this at the OMSF symposium. IA (chat) – we probably should have that conversation internally before we bring it openly in the workshop - there's a point to be made that we want to avoid a case where we further siphon money away from existing projects (centering on an existing project like openfold seems like a good idea) JW – I’d used DockPrep to very limited success before - It does seem to be a more open solution, though the quality is a bit rough.
JW + RG + IA – In person meeting planning We’ll push for it to be on day 1. Failing that, we’ll run it at the end of day 2 (starting 3:30/4 PM) - OFE will be running hands-on session in the AM to get EU folks involved. RG – Will be looking for a lot of feedback during our hands-on sessions, like understanding compute platforms/workflow tools Ways to avoid splitting rooms on day 2? OpenFE will have the “product announcement morning”, OpenFF will have the “product announcement afternoon” OFE stuff on day 3? Looked at registrations, will be ~5 industry

Action items

Decisions