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Posts by OMSF

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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 ...

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...

8 months ago 3 1 0 0

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!

11 months ago 7 2 0 0
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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...

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...

11 months ago 2 1 0 0

@ethanholz.com delivers! read more below

11 months ago 3 1 0 0
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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...

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.

11 months ago 6 2 0 1
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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.

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

1 year ago 9 1 1 2
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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...

WOW. thanks all to registered!

1 year ago 0 0 0 0
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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-...

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.

1 year ago 4 2 0 1
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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...

check out our Project Updates for the month!

1 year ago 2 1 0 1
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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!

#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...

1 year ago 3 4 0 0
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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...

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!

1 year ago 3 1 0 1
Boltz-1 and the Future of Biomolecular Foundation Models
Boltz-1 and the Future of Biomolecular Foundation Models YouTube video by Boston Protein Design and Modeling Club

@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:

1 year ago 2 1 0 0

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

1 year ago 1 0 0 0

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

1 year ago 0 0 0 0
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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...

if you are new to OMSF, we have a monthly newsletter to get you up to speed. check it out here:

1 year ago 2 2 1 0
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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...

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...

1 year ago 3 2 0 0
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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 ...

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??

1 year ago 3 1 1 1
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Winter RosettaCon Harvard Medical School

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

1 year ago 0 0 0 0
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...

happy to say it - our projects are hiring again!

1 year ago 1 1 0 0

how'd you do?

1 year ago 2 0 0 0
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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...

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!

1 year ago 2 3 0 0

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!

1 year ago 3 4 0 0
Physics-aware agentic artificial intelligence to model, design and discover proteins
Physics-aware agentic artificial intelligence to model, design and discover proteins YouTube video by Boston Protein Design and Modeling Club

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!

1 year ago 3 0 0 0
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.

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.

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...

1 year ago 30 14 0 0
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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...

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!

1 year ago 1 0 0 0
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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...

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!

1 year ago 8 6 0 1
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...

check out this write up from our very own @mattwthompson.bsky.social - some great advice from an expert

1 year ago 2 0 0 0
Careers About OMSF The Open Molecular Software Foundation (OMSF) is a US-based 501(c)(3) nonprofit organization focused on facilitating collaboration and software development for molecular sciences. OMSF aims...

Looking for something to do this weekend? Why not apply to be our next Data Curation expert?

1 year ago 1 1 0 0

Shoutout to @polarishub.io and @asapdiscovery.bsky.social - we are proud to have partners like you 💪

1 year ago 2 0 1 0
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Challenge: Revolutionizing Small Molecule Drug Discovery The Open Molecular Software Foundation (OMSF) OpenADMET project is proud to collaborate with the ASAP Discovery Consortium to launch an exciting computational blind challenge in small molecule drug di...

If you woke up today and thought, "hm, I'd really like to compete against the best and brightest in a robust, friendly drug discovery challenge that pushes the envelope of what open science is capable of," then we have great news for you!

1 year ago 14 5 1 0