Open Free Energy
@openfree.energy
Pinned
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...
Reposted by Open Free Energy
Jeff Wagner and Jen Clark ran a workshop at the @mdanalysis.bsky.social UGM in Arizona last week, in coordination with the @openfree.energy team.
November 17, 2025 at 4:43 PM
Jeff 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 command line interface (CLI) is designed to provide easy access to our tested, production-ready workflow. But if you are developing new methods or pioneering workflows, you may need the power and flexibility of our application programming interface (API) in #Python. #compchem
November 11, 2025 at 2:55 PM
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...
openfree.energy/science/upda...
openfe v1.7.0: SepTop, ABFEs, faster simulations, and more!
We are pleased to announce the release of openfe version 1.7.0!
openfree.energy
October 24, 2025 at 5:20 PM
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...
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!
October 14, 2025 at 5:41 PM
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 Energy
We’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.
October 10, 2025 at 3:02 PM
We’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 Energy
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!
September 23, 2025 at 5:36 PM
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!
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...
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
September 11, 2025 at 2:53 PM
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...
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
BespokeFit: Using bespoke force field parameters with OpenFE protocols — OpenFE documentation
docs.openfree.energy
August 27, 2025 at 7:25 PM
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
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
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
June 17, 2025 at 3:59 PM
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
www.deepmirror.ai/post/boltz-2...
#opensource #compchem #boltz2
It's exciting to see our software used as a benchmark for cutting-edge AI methods!
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!
June 13, 2025 at 1:01 AM
It's exciting to see our software used as a benchmark for cutting-edge AI methods!
Reposted by Open Free Energy
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!
May 27, 2025 at 11:27 PM
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!
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
#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
May 15, 2025 at 2:00 PM
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
#compChem
Reposted by Open Free Energy
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
May 9, 2025 at 6:51 PM
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
Reposted by Open Free Energy
@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!
May 9, 2025 at 6:46 PM
@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!
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
April 30, 2025 at 1:20 AM
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
openfree.energy/release/2025...
#opensource #compchem
April 29, 2025 at 4:00 PM
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
openfree.energy/release/2025...
#opensource #compchem
Reposted by Open Free Energy
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
April 22, 2025 at 10:24 PM
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.
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...
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
April 1, 2025 at 4:20 PM
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...
chemrxiv.org/engage/chemr...
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
#opensource #compchem
Tutorials — OpenFE documentation
docs.openfree.energy
March 26, 2025 at 1:54 AM
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
#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...
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
March 11, 2025 at 4:34 PM
#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
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
The Open Free Energy library
What's Changed Move CLI README so that it's easier to find by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1009 Add release checklist by @atravitz in https://github.com/OpenFreeEnergy/op...
doi.org
February 19, 2025 at 9:28 PM
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
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
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...
alchemiscale roadmap 2025
It’s 2025, and this month the project now known as alchemiscale celebrates its 3rd anniversary since kicking off in 2022.
alchemiscale.org
February 12, 2025 at 2:43 AM
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.
Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations
Alchemical free energy campaigns can be planned using graph theory by building networks that contain nodes representing molecules that are connected by possible transformations as edges. We introduce ...
pubs.acs.org
February 11, 2025 at 4:51 PM
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.
Reposted by Open Free Energy
if you didn't see it before, you're seeing it now - we are back for OMSF 2025!
and this year, we're in Boston. you can register now!
and this year, we're in Boston. you can register now!
Announcing OMSF Symposium 2025
It's time to mark your calendars!
The Open Molecular Software Foundation is headed to Boston, MA on Friday, May 9th, 2025 for our third symposium! We will be hearing from all of our team and projects...
news.omsf.io
January 31, 2025 at 4:16 PM
if you didn't see it before, you're seeing it now - we are back for OMSF 2025!
and this year, we're in Boston. you can register now!
and this year, we're in Boston. you can register now!
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...
February 4, 2025 at 2:46 PM
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...