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OMSF Project News - February 2025


Hello! As we move closer into the thick of 2025, we’re excited to share updates on our growing projects, new hires, and ongoing research milestones. Let’s take a moment to highlight the latest advancements across the OMSF community. Thanks for reading!

Staff Announcements

Welcome Sean Colby to the OpenADMET team! Coming to us from Pacific Northwest National Labs, Sean will be diving into chemical space exploration and ADMET model development.

This month, we say goodbye to Sam Curtis. After making significant contributions to the Rosetta Commons community, Sam has moved on to a government position in science policy. Open Force Field is also bidding farewell to Brent Westbrook, who is on to Rust-ier pastures at Astral!

Open Free Energy (OpenFE)

The OpenFE team has been making strides in refining its tools and workflows, focusing on usability and performance improvements. The 1.3 release introduced several quality-of-life updates, such as

  • Streamlined CLI 
  • Pymbar 4 support 
  • Reduced trajectory file size

Documentation updates continue, particularly for the Open Free Energy development API gufe. Meanwhile, early industry benchmarking efforts show promise. The team is also continuing efforts to benchmark different force fields, including evaluating the use of Bespokefit refined parameters. Stay tuned for the details!

OpenADMET

OpenADMET is growing quickly, with new funding allowing for expanded initiatives. And the team is working quickly too, shifting from dataset curation to modeling architecture, continuing its ongoing collaboration with Octant Bio to optimize synthesis workflows.

A major focus has been on a new machine learning workflow an automated ADMET model training framework.

Additionally, the team is co-hosting a blind challenge with ASAP AViDD and Polaris on predicting ligand poses, potency and ADMET properties for small molecules, which has already seen over 100 downloads and a dozen submissions. Among other prizes, a special JCIM issue dedicated to this blind challenge is being discussed with the editors and participants will be invited to submit their findings. Check it out here.

Looking for your next opportunity? OpenADMET is hiring for a Research Software Engineer. Learn more here.

OpenRosetta / RosettaCommons

RosettaCommons is hiring for two fully remote roles to support the development and usability of Rosetta and Rosetta-related AI tools in biomolecular design and modeling.

The community is also preparing for Winter RosettaCon which promises an excellent week of workshops and talks from all across the Commons. The REU Program, a community-wide Research Experience for Undergraduates,  saw a record-breaking 600+ applicants for just 20 spots, underscoring the continuing interest in Rosetta Commons initiatives.

Governance and communication improvements remain a priority, along with new educational initiatives such as the Biodesign in Focus YouTube series. Watch the latest sessions here or read the latest blog post.

Open Force Field

Please fill out the Interchange survey if you haven’t already! This will help guide OpenFF in improving its interoperability with other molecular simulation software.

OpenFF has a quick message for you all:

Ever wanted to simulate a covalent drug bound to a protein? A glyco- or lipo-protein? We have good news for you! Open Force Field just released a prototype of its officially supported Post-Translational Modification (PTM) modeling workflow for proteins. This uses ff14SB parameters for the canonical amino acids and Sage parameters (with NAGL charges) for the non-canonical residues. While this workflow is able to automate a lot of the complexity of handling PTMs, loading PDB files into cheminformatics representations is still a sticking point. To help with this we’ve made the openff-pablo package, and this notebook serves as an introduction to its functionality and a solicitation for future development directions. Please try the PTM workflow out and give us your feedback! There’s still some flexibility in our implementation, but we need to know what you need to guide our future development.

The Open Force Field team held its first internal on-site meeting in February in Irvine, CA! The team and wider initiative shared updates on many in-progress projects and engaged in  technical deep dives, research progress reports, and roadmap planning sessions. Most importantly, it was great for the team to connect with everyone that could make it both in-person and on Zoom. Be sure to check out Open Force Field's socials for pictures!

Thank you for being part of the OMSF community! We look forward to another successful year of collaboration and innovation. See you next month!

Published by:

Zachary Baker