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openfree.energy
Open Free Energy
@openfree.energy
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openfree.energy
Open Free Energy @openfree.energy · Feb 4
We're changing the field of #compchem by creating free and open-source software for performing alchemical free energy calculations. Our flagship protocol calculates relative binding free energies of protein-ligand systems. Try it out in your browser: colab.research.google.com/github/OpenF...
Artistic rendering of a biochemical model: a small molecule ligand, shown as a ball-and-stick model colored by element, is bound in a pocket in a protein surface, shown as a space filling model colored off-white.
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Reposted by Open Free Energy
feworkshop.bsky.social
Free Energy Workshop 2025 @feworkshop.bsky.social · 15d
Save 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!
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openfree.energy
Open Free Energy @openfree.energy · 27d
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...
Optimizing Molecular Glues Using Free Energy Perturbation and Cofolding Methods
Molecular glues, a class of small molecules that induce protein-protein interactions, hold significant promise as a therapeutic modality, offering access to new biology unlocking new protein targets w...
chemrxiv.org
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openfree.energy
Open Free Energy @openfree.energy · Aug 27
You can find more information starting on slide 20 in our February 2025 update presentation: zenodo.org/records/1486...
zenodo.org
openfree.energy
Open Free Energy @openfree.energy · Aug 27
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.
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openfree.energy
Open Free Energy @openfree.energy · Aug 27
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.
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openfree.energy
Open Free Energy @openfree.energy · Aug 27
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
BespokeFit: Using bespoke force field parameters with OpenFE protocols — OpenFE documentation
docs.openfree.energy
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openfree.energy
Open Free Energy @openfree.energy · Aug 19
This is such cool work. Ivan from the Chodera Lab is implementing a protein mutation protocol in OpenFE, and we can't wait to see what incredible studies people do with it!
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openfree.energy
Open Free Energy @openfree.energy · Jun 24
It's great to see this work in print! It's not on our roadmap this year, but in the longer term we are interested in optimizing replica spacing and will look closely at your method.
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openfree.energy
Open Free Energy @openfree.energy · Jun 17
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/...
Boltz-2 vs. FEP? The Wrong Question. Here’s Why They’re Stronger Together
The Boltz-2 AI model lays claim to some amazing improvements in ligand affinity prediction. The greatest value may be in the realms of…
medium.com
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openfree.energy
Open Free Energy @openfree.energy · Jun 17
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
Evaluating Boltz-2 on Real Drug Targets: Does it work? | deepmirror
Evaluating Boltz-2 on Real Drug Targets: Does it work?
www.deepmirror.ai
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openfree.energy
Open Free Energy @openfree.energy · Jun 13
It's exciting to see our software used as a benchmark for cutting-edge AI methods!
gcorso.bsky.social
Gabriele Corso @gcorso.bsky.social · Jun 6
On the standard FEP+ affinity benchmark, whose targets were held out of training, Boltz-2 achieves an average Pearson of 0.62—comparable to OpenFE, a widely adopted open-source FEP pipeline, while being over 1000x faster!
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Reposted by Open Free Energy
dotsdl.bsky.social
David L. Dotson @dotsdl.bsky.social · May 27
This poster illustrates the substantial flexibility of the open source @openfree.energy ecosystem, enabling unconventional approaches for applying free energy methods. As this ecosystem continues to evolve, I'm excited to see what users do with the advancements we make!
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openfree.energy
Open Free Energy @openfree.energy · May 15
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
The Free Energy of Everything: Benchmarking OpenFE
Written by: Josh Horton, PhD Who is OpenFE and what do they do? Open Free Energy (OpenFE) sits at the nexus of academia and industry. We are developing an open-source software ecosystem for alchem...
blog.omsf.io
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Reposted by Open Free Energy
Karmen Condic-Jurkic @karmencj.bsky.social · May 9
Aniket Margakar from Boehringer demonstrated how they use @omsf.io tools in house, praising both the tools and teams -- that's what we like to hear! He highly recommends NAGL and bespokefit for fast charge assignment and parameterization, and @openfree.energy for FE calcs
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Reposted by Open Free Energy
Karmen Condic-Jurkic @karmencj.bsky.social · May 9
@jenkescheen.bsky.social showcased his work on @asapdiscovery.bsky.social and more recently with CharmTx, combining ML and more traditional free energy calculations. A lot, if not all, of his work is based on @openfree.energy, #openforcefield, and #alchemsicale. Read his papers for more details!
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openfree.energy
Open Free Energy @openfree.energy · Apr 30
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-...
Introducing OMSF Self-Hosted Runners
Written by: Ethan Holz Today marks the official launch of almost a year of work from the OMSF Ecosystem Infrastructure team to deliver a solution for Self-Hosted GitHub Actions runners. This directiv...
blog.omsf.io
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openfree.energy
Open Free Energy @openfree.energy · Apr 30
Thanks for your great work on this project. We love the result!
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openfree.energy
Open Free Energy @openfree.energy · Apr 29
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
A screenshot from the linked page, which reads "An example of how a results table might look as of v1.4.0)" and shows a cleanly-formatted table, including borders.
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Reposted by Open Free Energy
omsf.io
OMSF @omsf.io · Apr 22
in his blog, our very own Mike Henry demonstrates a powerful, useful skill - CONTAINERIZING. if you are looking for a good how-to on packaging tools, look no further.
Dockerize a Tool
Written by: Mike Henry, PhD Source: https://www.henrymike.com/dockerize-a-tool.html Curious about how to containerize your scientific tools for smoother collaboration and deployment? In this post, Mi...
blog.omsf.io
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openfree.energy
Open Free Energy @openfree.energy · Apr 1
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!
openfree.energy
Open Free Energy @openfree.energy · Apr 1
Their framework was as accurate as approaches that use conventional docking methods, while being much faster.
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openfree.energy
Open Free Energy @openfree.energy · Apr 1
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...
Leveraging Alchemical Free Energy Calculations with Accurate Protein Structure Prediction
Small-molecule lead optimisation in early-stage drug discovery is broadly supported by computational chemistry approaches throughout industry. Over the last decade, Free Energy Perturbation (FEP) has ...
chemrxiv.org
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openfree.energy
Open Free Energy @openfree.energy · Mar 26
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
Tutorials — OpenFE documentation
docs.openfree.energy
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Reposted by Open Free Energy
openfold.io
OpenFold @openfold.io · Mar 11
#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...
Proteomics Playbook 2025 - Front Line Genomics
We hope that this report inspires you to tackle proteomics in your own work and help drive advancements in this exciting field!
frontlinegenomics.com
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openfree.energy
Open Free Energy @openfree.energy · Mar 4
The purely technical problems in our field (#compchem) have all been solved by PhD students working alone. We are here to tackle the social problems.