Lightnews — Scholar-powered news

OMSF @omsf.io · Jul 28

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...

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

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OMSF @omsf.io · May 9

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!

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OMSF @omsf.io · May 2

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 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

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OMSF @omsf.io · Apr 30

@ethanholz.com delivers! read more below

Ethan Holz @ethanholz.com · Apr 29

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-...

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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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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Reposted by OMSF

OpenFold @openfold.io · Apr 15

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

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

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OMSF @omsf.io · Apr 8

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

OMSF @omsf.io · Apr 1

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.

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

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OMSF @omsf.io · Mar 27

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

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Reposted by OMSF

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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OMSF @omsf.io · Mar 11

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

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OMSF @omsf.io · Mar 10

@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

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OMSF @omsf.io · Mar 4

this three ain't just a crowd, it's a party!

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OMSF @omsf.io · Mar 4

you can always subscribe to the Newsletter to get the news hot of the press!

OMSF @omsf.io · Mar 4

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

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OMSF @omsf.io · Feb 28

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...

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

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OMSF @omsf.io · Feb 25

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

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OMSF @omsf.io · Feb 24

in just 2 short days, Winter RosettaCon kicks off. are you going??

Winter RosettaCon

Harvard Medical School

winterrosettacon.org

OMSF @omsf.io · Feb 20

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

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OMSF @omsf.io · Feb 18

how'd you do?

Polaris @polarishub.io · Feb 17

⚡ 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

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OMSF @omsf.io · Feb 11

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

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Reposted by OMSF

Cole Group @colegroupncl.bsky.social · Jan 29

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!

The ASAP Discovery Consortium @asapdiscovery.bsky.social · Jan 15

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!

Polaris @polarishub.io · Jan 14

🏁 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. 🧑‍💻

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OMSF @omsf.io · Feb 7

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!

Physics-aware agentic artificial intelligence to model, design and discover proteins

YouTube video by Boston Protein Design and Modeling Club

www.youtube.com

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Reposted by OMSF

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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OMSF @omsf.io · Feb 4

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

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