@openfree.energy
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pinned post!
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...
8 months ago
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reposted by
Free Energy Workshop 2025
4 days ago
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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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...
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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...
https://chemrxiv.org/engage/chemrxiv/article-details/68bad5e3728bf9025e961742
17 days ago
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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
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BespokeFit: Using bespoke force field parameters with OpenFE protocols β OpenFE documentation
https://docs.openfree.energy/en/latest/cookbook/bespoke_parameters.html
about 1 month ago
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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
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Evaluating Boltz-2 on Real Drug Targets: Does it work? | deepmirror
Evaluating Boltz-2 on Real Drug Targets: Does it work?
https://www.deepmirror.ai/post/boltz-2-real-drug-targets
3 months ago
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It's exciting to see our software used as a benchmark for cutting-edge AI methods!
add a skeleton here at some point
4 months ago
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reposted by
David L. Dotson
4 months ago
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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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 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...
https://blog.omsf.io/the-free-energy-of-everything-benchmarking-openfe/
5 months ago
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reposted by
Karmen Condic-Jurkic
5 months ago
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
Karmen Condic-Jurkic
5 months ago
@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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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-...
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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...
https://blog.omsf.io/introducing-omsf-self-hosted-runners/
5 months ago
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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
5 months ago
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reposted by
OMSF
5 months ago
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.
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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...
https://blog.omsf.io/dockerize-a-tool/
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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...
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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 ...
https://chemrxiv.org/engage/chemrxiv/article-details/67d3ea816dde43c908c21ba4
6 months ago
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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
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Tutorials β OpenFE documentation
https://docs.openfree.energy/en/stable/tutorials/index.html
6 months ago
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reposted by
OpenFold
7 months ago
#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...
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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!
https://frontlinegenomics.com/proteomics-playbook-2025/
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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
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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...
https://doi.org/10.5281/zenodo.14889827
7 months ago
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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...
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alchemiscale roadmap 2025
Itβs 2025, and this month the project now known as alchemiscale celebrates its 3rd anniversary since kicking off in 2022.
https://alchemiscale.org/roadmaps/alchemiscale-2025/
8 months ago
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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.
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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 ...
https://pubs.acs.org/doi/10.1021/acs.jcim.4c01710
8 months ago
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reposted by
OMSF
8 months ago
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!
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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...
https://news.omsf.io/announcing-omsf-symposium-2025/
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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...
8 months ago
0
30
14
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