Open Free Energy
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- Reposted by Open Free EnergyOpenBind is a new open science effort to dramatically increase the number of protein:ligand structures in the PDB, pairing this with high-quality affinity data to enable a new generation of predictive structure and affinity models for drug discovery. Check it out: openbind.ai
- Join our mailing list for early access to AI-driven drug discovery insights & breakthroughs through the #OpenBind initiative. loom.ly/Vro7Lo8
- Reposted by Open Free EnergyExciting news! We have a new website: omsf.io/alchemistry Your one-stop shop for everything related to our conference community. 🎉 BTW, registration is now open, so head over to secure your spot! We'll be sharing updates and details about the event. Bookmark it as there's plenty more to come!
- OpenFE is ready for production! chemrxiv.org/engage/chemr... In collaboration with our industry partners, we ran benchmarking simulations of our hybrid-topology RBFE protocol on a large collection of both public and private protein-ligand binding datasets. #compchem
- Across a total of 1,700 ligands, OpenFE shows robust performance, generates reproducible results, and achieves both sufficient throughput and rapid convergence. Our protocol: - ranks compounds about as well as commercial solutions - does not require fine-tuning settings for each system
- To our knowledge, this is the first study to report binding free energy benchmarks on a cross-company collection of proprietary datasets. We couldn't have done it without the hard work of our amazing partner companies!
- Reposted by Open Free EnergyJeff Wagner and Jen Clark ran a workshop at the @mdanalysis.bsky.social UGM in Arizona last week, in coordination with the @openfree.energy team.
- Our docs have you covered! We have a "cookbook" demonstrating how to use our API for a variety of tasks in setting up free energy calculations. docs.openfree.energy/en/latest/co...
- We've just released openfe v1.7, which includes includes new protocols for Separated Topologies and Absolute Binding Free Energies, as well as up to 2x faster simulations using the default settings. openfree.energy/science/upda...
- We tested Sage 2.3.0rc2 from @openforcefield.org in RBFE benchmarks and found it improves accuracy on some of our benchmark systems like p38. Can't wait to see the GNN charge model become default!
- Reposted by Open Free EnergyWe’re pleased to announce Sage 2.3.0 Release Candidate 2 (rc2)! Sage 2.3.0 will be the first OpenFF force field to use the AshGC neural network charge model, which was trained to AM1BCC ELF10 charges, and allows for rapid charge assignment for molecules with hundreds or thousands of heavy atoms.
- Reposted by Open Free EnergySave the date, my fellow computational alchemists! The upcoming '26 Workshop on Free Energy Methods in Drug Design will be held in Barcelona, Spain, on May 4-6, 2026. The registration link will be sent soon!
- OpenFE is being used to predict affinity of molecular glues! Check out the new preprint from the team at Ternary Therapeutics: chemrxiv.org/engage/chemr...
- Did you know you can use custom force field parameters in OpenFE? Try out this cookbook to learn more! docs.openfree.energy/en/latest/co... #compchem
- Our default force field, OpenFF “Sage,” works well on a wide variety of organic molecules relevant to drug design. However, projects involving more exotic functional groups may be limited by low force field accuracy.
- To address these challenging cases, the Open Force Field Intitiative provides a tool, “BespokeFit,” for generating custom parameters for the specific chemistry of a target molecule. These custom (or “bespoke”) parameters can be used in RBFE calculations in OpenFE.
- You can find more information starting on slide 20 in our February 2025 update presentation: zenodo.org/records/1486...
- Alchemical free energy simulations will remain a crucial step in teh drug design process for their accuracy and reliability, especially in binding pockets that rearrange to accommodate different ligands. www.deepmirror.ai/post/boltz-2... #opensource #compchem #boltz2
- But the ability of Boltz-2 to predict affinity opens up new possibilities for drug design workflows, like the Affinity Funneling approach that David Pearlman describes here. medium.com/@dapscience/...
- It's exciting to see our software used as a benchmark for cutting-edge AI methods!
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- If you weren't at @feworkshop.bsky.social in Boston last week, you missed Hannah Baumann giving the first sneak peek at results from our partner benchmarking study! Fortunately for you, Josh Horton wrote up a blog post about the early results: blog.omsf.io/the-free-ene... #compChem
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- The Ecosystem Infrastructure team at @omsf.io (@ethanholz.com and David Swenson) built a tool for running github actions on self-hosted runners. Not the first such tool anyone's ever built, but designed to meet the particular needs of our community, and they delivered! blog.omsf.io/introducing-...
- We just dropped a new minor release of the openfe software, v1.4.0! It adds several quality-of-life improvements to the command line interface, especially to the `gather` command. openfree.energy/release/2025... #opensource #compchem
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- Researchers at Charm Therapeutics have developed a hybrid framework for small molecule lead optimization in early-stage #DrugDiscovery. It incorporates both an #AI co-folding method and our protocol for calculating relative binding free energies. chemrxiv.org/engage/chemr...
- Their framework was as accurate as approaches that use conventional docking methods, while being much faster.
- They report that "The output structures of [AI co-folding model] DragonFold can be readily ported into OpenFE with minimal post-processing." We are glad to hear this feedback, and congratulations on this exciting work!
- Ready to start using OpenFE? Our documentation includes tutorials on how to use different aspects of our tooling: docs.openfree.energy/en/stable/tu... #opensource #compchem
- Reposted by Open Free Energy#OpenFold was highlighted in the #ProteomicsPlaybook from Front Line Genomics. You can hear from our co-founder, @lucasnivon.bsky.social, and our business manager, Mallory Tollefson, to learn about why our consortium began and where we are going. frontlinegenomics.com/proteomics-p...
- New minor release of our software! openfe v1.3.0 includes a number of quality-of-life enhancements, including new CLI features and reduced file size for saved trajectories. doi.org/10.5281/zeno... #openSource #compChem
- See the changelog here: docs.openfree.energy/en/stable/CH...
- Our colleagues at Datryllic, LLC lead the development of Alchemiscale, a distributed execution system for our protocols. They just released a roadmap for how to get to a feature-complete v1.0.0 release this year! alchemiscale.org/roadmaps/alc...
- Our partnership with @boehringerglobal.bsky.social has been very productive. Last year, Benjamin Ries published scientific papers describing two different tools for setting up alchemical simulations, that he built as a contributor to our team. These tools are now integral to our RBFE protocol.
- The more recent one, Konnektor, is a toolbox for applying graph theory operations to networks of molecular transformations, as we use to calculate Relative Binding Free Energies. These tools open up new possibilities for planning large simulation campaigns. konnektor.readthedocs.io/en/latest/
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