OMSF
@omsf.io
the Open Molecular Software Foundation is dedicated to the creation and implementation of the latest and greatest open comp.chem software.
we have a blog - and there's some great stuff on it!
check out this post by David Mobley. who knows, maybe we can say bye to aromaticity in our force fields?
blog.omsf.io/why-we-shoul...
check out this post by David Mobley. who knows, maybe we can say bye to aromaticity in our force fields?
blog.omsf.io/why-we-shoul...
Why We Should Drop (Graph-based) Bond Order and No Longer Use Aromaticity
Written by: David Mobley, PhD
OpenFF force fields assign parameters based on queries operating on the chemical graph for molecules, via the SMARTS language. This language is rather flexible, leaving ...
blog.omsf.io
July 28, 2025 at 7:34 PM
we have a blog - and there's some great stuff on it!
check out this post by David Mobley. who knows, maybe we can say bye to aromaticity in our force fields?
blog.omsf.io/why-we-shoul...
check out this post by David Mobley. who knows, maybe we can say bye to aromaticity in our force fields?
blog.omsf.io/why-we-shoul...
we are having a blast! keynotes from @openfree.energy , @openfold.io , and @openadmet.bsky.social, and Open Force Field have been stellar. @lilyminium.bsky.social and @ialibay.bsky.social - we are so proud!
May 9, 2025 at 3:41 PM
we are having a blast! keynotes from @openfree.energy , @openfold.io , and @openadmet.bsky.social, and Open Force Field have been stellar. @lilyminium.bsky.social and @ialibay.bsky.social - we are so proud!
hey all - we gather in Boston in ONE.WEEK. all the people we only see in screens, in one room, in person for a day of science and community. find all the relevant information here!
omsf.notion.site/OMSF-Symposi...
omsf.notion.site/OMSF-Symposi...
OMSF Symposium 2025 | Notion
May 9th, 2025 - OMSF is back for our third annual symposium! We are excited to share an incredible day with you. We begin our day on the front lines of open molecular modeling, with words from our sof...
omsf.notion.site
May 2, 2025 at 8:32 PM
hey all - we gather in Boston in ONE.WEEK. all the people we only see in screens, in one room, in person for a day of science and community. find all the relevant information here!
omsf.notion.site/OMSF-Symposi...
omsf.notion.site/OMSF-Symposi...
@ethanholz.com delivers! read more below
Hey everyone! My @omsf.io published my post about why we built a GitHub Actions solution for provisioning self-hosted runners on different clouds! Let us know what you think!
blog.omsf.io/introducing-...
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 4:05 PM
@ethanholz.com delivers! read more below
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.
Reposted by OMSF
Our new member press release is out! We’re thrilled to welcome 8 new partners to the OpenFold Consortium.
Full announcement here:
www.businesswire.com/news/home/20...
Please share & help us welcome the newest members of our community! 🤝 #OpenFold #AI #OpenScience
Full announcement here:
www.businesswire.com/news/home/20...
Please share & help us welcome the newest members of our community! 🤝 #OpenFold #AI #OpenScience
OpenFold AI Research Consortium Welcomes New Members Including Bristol Myers Squibb, COGNANO, Lambda, Novo Nordisk, Structure Therapeutics, Tamarind, Unnatural Products, and Visterra
OpenFold continues to expand its collaborative network of academic and industry leaders for the advancement of open-source AI in molecular sciences.
www.businesswire.com
April 15, 2025 at 2:41 PM
Our new member press release is out! We’re thrilled to welcome 8 new partners to the OpenFold Consortium.
Full announcement here:
www.businesswire.com/news/home/20...
Please share & help us welcome the newest members of our community! 🤝 #OpenFold #AI #OpenScience
Full announcement here:
www.businesswire.com/news/home/20...
Please share & help us welcome the newest members of our community! 🤝 #OpenFold #AI #OpenScience
WOW. thanks all to registered!
OMSF Symposium 2025: Updates
Unbelievable.
OMSF Symposium 2025 is one month away!
Thanks to the incredible interest from across the community, registration for the OMSF Symposium 2025 is now closed. We’ve officially hit capacit...
news.omsf.io
April 8, 2025 at 4:17 PM
WOW. thanks all to registered!
the longest journey begins with a single step. luckily for us, @arianaclerkin.bsky.social is writing hers down!
read the first PLUMB blab of many below, and follow along as Ariana builds an open comp.chem project from the ground up.
read the first PLUMB blab of many below, and follow along as Ariana builds an open comp.chem project from the ground up.
PLUMB blab #1: We need better benchmarks for computer-aided drug design
Written by: Ariana Brenner Clerkin, PhD
Welcome to a new series on the OMSF blog: PLUMB blab! This series will take you behind the scenes of PLUMB (Protein-Ligand Unified Metrics Benchmark), an open-...
omsf-blog.ghost.io
April 1, 2025 at 3:14 PM
the longest journey begins with a single step. luckily for us, @arianaclerkin.bsky.social is writing hers down!
read the first PLUMB blab of many below, and follow along as Ariana builds an open comp.chem project from the ground up.
read the first PLUMB blab of many below, and follow along as Ariana builds an open comp.chem project from the ground up.
check out our Project Updates for the month!
OMSF Project News - March 2025
Greetings! We at OMSF hope you are having a wonderful year so far. As we move into spring, we’d like to dose you with our monthly OMSF project updates.
Staff Announcements
Mallory Tollefson has be...
news.omsf.io
March 27, 2025 at 5:44 PM
check out our Project Updates for the month!
Reposted by OMSF
#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...
our next blog comes from James Eastwood, PM over at Open Force Field. he'll sum up the last 6 months of the project - get your history here!
What's up with OpenFF?
Written by: James Eastwood, PhD
The past few months have been somehow both busy and quiet for the staff of OpenFF. We’ve said goodbye to some old colleagues and hello to new. We’ve been improving ou...
omsf-blog.ghost.io
March 11, 2025 at 3:17 PM
our next blog comes from James Eastwood, PM over at Open Force Field. he'll sum up the last 6 months of the project - get your history here!
@bpdmc.bsky.social hosts those on the bleeding edge of molecular modeling. if you want to know what's what, check out their YouTube page. here's the latest presentation:
Boltz-1 and the Future of Biomolecular Foundation Models
YouTube video by Boston Protein Design and Modeling Club
www.youtube.com
March 10, 2025 at 3:44 PM
@bpdmc.bsky.social hosts those on the bleeding edge of molecular modeling. if you want to know what's what, check out their YouTube page. here's the latest presentation:
if you are new to OMSF, we have a monthly newsletter to get you up to speed. check it out here:
OMSF Project News - February 2025
Hello! As we move closer into the thick of 2025, we’re excited to share updates on our growing projects, new hires, and ongoing research milestones. Let’s take a moment to highlight the latest advance...
news.omsf.io
March 4, 2025 at 5:04 PM
if you are new to OMSF, we have a monthly newsletter to get you up to speed. check it out here:
another open position! OpenADMET is looking for Research Software Engineers to help with some lifting. hit the jump to learn more!
omsf.io/community/jo...
omsf.io/community/jo...
Job Board
All OMSF positions are currently remote, and we generally accept applications worldwide. Some positions may be restricted to the United States. All positions require a valid work permit - OMSF has lim...
omsf.io
February 28, 2025 at 5:07 PM
another open position! OpenADMET is looking for Research Software Engineers to help with some lifting. hit the jump to learn more!
omsf.io/community/jo...
omsf.io/community/jo...
in the most recent OMSF blog, Hugo MacDermott-Opeskin asks the important question: if we don't have nice things, where can we get them??
How Geoscience Can Help Fix Molecular Simulation’s Data Problem
Written by: Hugo MacDermott-Opeskin, PhD
Source: https://hmacdope.github.io/posts/geoscience_molecular_simulation/
We can and should do better.
TLDR: Molecular simulation can enter its big-data era ...
omsf-blog.ghost.io
February 25, 2025 at 2:50 PM
in the most recent OMSF blog, Hugo MacDermott-Opeskin asks the important question: if we don't have nice things, where can we get them??
in just 2 short days, Winter RosettaCon kicks off. are you going??
Winter RosettaCon
Harvard Medical School
winterrosettacon.org
February 24, 2025 at 3:20 PM
in just 2 short days, Winter RosettaCon kicks off. are you going??
happy to say it - our projects are hiring again!
Job Board
All OMSF positions are currently remote, and we generally accept applications worldwide. Some positions may be restricted to the United States. All positions require a valid work permit - OMSF has lim...
omsf.io
February 20, 2025 at 9:57 PM
happy to say it - our projects are hiring again!
how'd you do?
⚡ The intermediate leaderboard for the antiviral challenge is now live!
👀 See how you placed: antiviral.polarishub.io
The challenge officially ends on March 10th, but there's one last leaderboard update before the final results.
Submit before midnight on Feb 26th! polarishub.io/competitions
👀 See how you placed: antiviral.polarishub.io
The challenge officially ends on March 10th, but there's one last leaderboard update before the final results.
Submit before midnight on Feb 26th! polarishub.io/competitions
February 18, 2025 at 3:09 PM
how'd you do?
one of our projects - Open Force Field - is looking for feedback on their Interchange software. this is your chance to influence the development of this killer product. let them know!
Interchange Stakeholder Survey
The OpenFF Infrastructure team is preparing to make a 1.0 release of Interchange and a roadmap that describes major project objectives leading up to and following the milestone. We want to hear from u...
docs.google.com
February 11, 2025 at 4:48 PM
one of our projects - Open Force Field - is looking for feedback on their Interchange software. this is your chance to influence the development of this killer product. let them know!
Reposted by OMSF
Our team is having fun trying out the binding pose challenge! Check it out below, the organisers have done a great job making the data easy to access and understand!
Working on predictive models for drug discovery? Here's your chance to see how well your models actually work!
Together with @polarishub.io and OpenADMET, we've launched a blind prospective challenge to see how well predictive models for drug discovery can actually predict real drug discovery data!
Together with @polarishub.io and OpenADMET, we've launched a blind prospective challenge to see how well predictive models for drug discovery can actually predict real drug discovery data!
🏁 The antiviral challenge is live! 🏁
Ready to test your skills on new data? Hosted in partnership with @asapdiscovery.bsky.social and @omsf.io, we've prepared detailed notebooks showcasing how to format your data and submit your solutions. 🧑💻
Ready to test your skills on new data? Hosted in partnership with @asapdiscovery.bsky.social and @omsf.io, we've prepared detailed notebooks showcasing how to format your data and submit your solutions. 🧑💻
January 29, 2025 at 5:54 PM
Our team is having fun trying out the binding pose challenge! Check it out below, the organisers have done a great job making the data easy to access and understand!
have you heard of @bpdmc.bsky.social ? these guys get together every month for pizza and protein modeling...our kind of group!
check out the presentation Markus Buehler gave last year. he explores how physics-aware AI is revolutionizing protein modeling. and if you find Markus here, tag him below!
check out the presentation Markus Buehler gave last year. he explores how physics-aware AI is revolutionizing protein modeling. and if you find Markus here, tag him below!
Physics-aware agentic artificial intelligence to model, design and discover proteins
YouTube video by Boston Protein Design and Modeling Club
www.youtube.com
February 7, 2025 at 5:17 PM
have you heard of @bpdmc.bsky.social ? these guys get together every month for pizza and protein modeling...our kind of group!
check out the presentation Markus Buehler gave last year. he explores how physics-aware AI is revolutionizing protein modeling. and if you find Markus here, tag him below!
check out the presentation Markus Buehler gave last year. he explores how physics-aware AI is revolutionizing protein modeling. and if you find Markus here, tag him below!
Reposted by OMSF
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...
quick throwback to 2023: we were so delighted to get our first NSF grant. it's made a huge impact on our ecosystem - addressing project needs and solving them with high-quality software. just a small taste of the power of funding open science!
NSF POSE: Phase II: Building open source ecosystems in molecular sciences through collaboration and technology
A redacted version of the full project description of the grant proposal submitted in Oct 2022 in response to NSF POSE solicitation. Results from prior NSF support section have been excluded from this...
zenodo.org
February 4, 2025 at 12:30 PM
quick throwback to 2023: we were so delighted to get our first NSF grant. it's made a huge impact on our ecosystem - addressing project needs and solving them with high-quality software. just a small taste of the power of funding open science!
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!
check out this write up from our very own @mattwthompson.bsky.social - some great advice from an expert
Six steps to success when reporting open-source computational chemistry issues
I’ve been working with open-source computational chemistry tools for about a decade, half of which has been in a professional capacity. I’ve worn about every hat - developer, maintainer, confused user...
mattthompson.dev
January 27, 2025 at 2:33 PM
check out this write up from our very own @mattwthompson.bsky.social - some great advice from an expert