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OMSF Project News - Holidays 2024

Merry Christmas! As 2024 comes to a close, we’re excited to share updates on our growing community, new projects, and major milestones. Let’s take a moment to welcome new faces, celebrate achievements, and look forward to what’s ahead.

Staff Announcements

Welcome, Jennifer Clark! We’re thrilled to welcome Jennifer Clark to the Open Force Field team. Jennifer will be focusing on QM datasets and an exciting organometallics collaboration with Genentech. Her expertise and enthusiasm will make a significant impact as we enter 2025.

Farewell! This month, we say goodbye to two valued team members. Benjamin Reis has departed from Open Free Energy, where his contributions to Kartograph played a vital role in the project's development and success. Similarly, Lexie McIsaac has moved on from Open Force Field to a startup, where she will hone her skills in machine learning. While we are going to miss them here, we’re excited to see what they accomplish in their new ventures and wish them the very best.

Open Free Energy

Open Free Energy has been busy refining its tools and workflows. Check out some of the releases below:

  • FE Flow v0.1.1: Bugfixes to improve the efficiency of the non-equilibrium cycling Protocol execution when deployed on Alchemiscale-FAH.
  • Kartograf v1.1.0 (coming soon!): Adds new atom mapping filters, such as ring hybridization, and introduces the ability to do protein mutation mappings.
  • Alchemiscale v0.5.3: Fixes Protocol filtering bugs, while the upcoming v0.6.0 will include result caching, at-rest compression, and task restart policies.

Research Milestones. Meghan Osato’s preprint on partial charge assignments and their impact on free energy calculations is now out on ChemRxiv: https://chemrxiv.org/engage/chemrxiv/article-details/67579833085116a133e39d86. This is the outcome of a research collaboration between the Mobley lab and Open Free Energy.

Open Fold

Get ready! The Open Fold team is preparing for a dress rehearsal to scale training runs to 32 nodes—a key step before starting production in early 2025. Alongside this technical push, the consortium continues to grow, doubling to 24 members this year. Congratulations OpenFold!

Call for Expertise. To unlock resources at Lawrence Livermore National Labs, Open Fold is seeking help converting CUDA kernels to AMD compatibility. If you know someone with expertise in this area, don't hesitate to reach out to Mallory Tollefson.

Open Force Field

The Open Force Field team has had a busy and productive end of the year, culminating in the completion of some seriously ambitious work. Highlights include:

  • Software Updates: The release of Interchange v0.4 introduced support for PyDantic 2, a major milestone in aligning OpenFF’s stack with Python libraries.
  • Quantum Chemistry and Protein Simulations: The team is crunching some of the largest QM optimizations to date, including molecules with up to 70 heavy atoms. Additionally, the team has launched GPU-enabled protein simulations on the National Research Platform, providing unprecedented access to compute resources, with up to 100 GPUs available at a time.
  • NAGL Charge Model: work continues on NAGL (Neural Assignments for Generalized Loads), which looks become it's own standalone charge model, one that enables more precise and tailored simulations.
  • Interoperability Advances: Significant progress has been made in improving interoperability, particularly with GROMACS.

As the year winds down, the team is tying up loose ends, releasing updates to their toolkit, and preparing for NAGL Phase 2. This next phase will expand the model’s capabilities to incorporate partial charges and address broader use cases.

Open ADMET

Open ADMET, a collaboration between UCSF, Octant, and OMSF, is off to a strong start. The team is curating its first dataset of 1,000 compounds focused on metabolism, with plans to iterate toward a 10,000-compound library.

The team is hiring for roles in data curation, machine learning, and pipeline automation. If you or someone you know is interested, learn more at openadmet.org.

Open Rosetta

The Rosetta community celebrated David Baker’s Nobel Prize in Stockholm with over 200 attendees, including members of Rosetta Commons, PIs, trainees, alumni, and industry leaders.

Upcoming Events

  • Winter Rosettacon (Feb 26–28, 2025) in Boston. Early registration ends Dec 31—register here.
  • Trainee Workshop (Jan 6–10, 2025) at UC Davis.

Open Rosetta is also enhancing communication with a new newsletter, recorded grad school info sessions, and updates to their playbooks and website. More information to come - stay tuned!

Looking Ahead: Events and Community

Virtual Winter School on Computational Chemistry. Launching January 2025, this event will connect computational chemistry enthusiasts worldwide. Learn more at winterschool.cc.

Alchemistry Workshop (May 6–8, 2025). The Free Energy workshop is in Boston this year, and is already looking for submissions and contributions. Interested in presenting a talk or poster? Submit your abstract here or contact Zachary Baker for assistance.

Thank you for your continued contributions to the OMSF community. Together, we’re pushing the boundaries of science and collaboration. Here’s to a successful 2025!

Published by:

Zachary Baker