Simon Mathis

Super cool work - congratulations @umbislupo.bsky.social & team!

Congratulations @chaitjo.bsky.social ! 🙌

Accelerating Biomolecular Modeling with AtomWorks and RF3 Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...

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Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)

[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)

RosettaFold 3 is here! 🧬🚀

AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!

Congratulations @simonmathis.bsky.social and team!!! ❤️

bioRxiv preprint: www.biorxiv.org/content/10.1...

This paper represents a great effort by @roman-bushuiev.bsky.social and his brother @anton-bushuiev.bsky.social. The DreaMS foundation model for mass spectra of small molecules now opens lots of avenues for possible downstream applications. It might be a game changer for computational metabolomics.

Very nice, thoughtful post - I really enjoyed the read @pascalnotin.bsky.social

🔥 Benchmark Alert! MotifBench sets a new standard for evaluating protein design methods in motif scaffolding.
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️

🚨Preprint Alert!🚨

#ProteinDesign is advancing rapidly—wouldn't it be great to seamlessly combine design tools to achieve more than what each can do alone?🤔

Here, we introduce AI.zymes: A modular platform for evolutionary #EnzymeDesign.♻️🖥️

biorxiv.org/content/10.1...
1/🧵

Amazing, congratulations @machine.learning.bio

You may have seen a recent pre-print [1] from Jain et al. with strongly worded claims against the experimental results in our DiffDock paper [2]. We initially declined to respond as we saw that this preprint contained falsehoods, misleading comparisons, seemingly deliberate omissions, ...1/n

Can AI improve the current state of molecular simulation? (Corin & Ari Wagen, Ep #1) 2.1 hours listening time

Can AI improve the current state of molecular simulation?

www.owlposting.com/p/can-ai-imp...

in my first podcast, I spend 2 hours interviewing Corin Wagen and Ari Wagen, two brothers who are building the next generation of molecular simulation for drug discovery and material science

Thank you for the feedback! That’s great to hear 🙌

(2/2) ... say a diffusion trajectory then it's doing something you cannot achieve by rsyncing folders (or only *very* cumbersomely). I mostly use it to debug & sanity check my code whilst developing for example

(1/2) Good question! If you only use it to look at static pymol files that you saved out then yes, it's an alternative to rsyncing your hpc folder. If you use it to for example visualize in-RAM objects during code execution / debugging, or if you use it to manually dock something midway through ...

We are hiring (resharing appreciated)!

Given recent successful grant applications (I got my SNSF Starting Grant 🚀), we are extending the LIAC team with multiple openings (PhD/postdoc) for 2025.

Apply now (deadline: December 20th) by filling in this form: forms.fillout.com/t/eq5ADAw3kkus.
#ChemSky

Thank you Greg! I actually found out about this functionality by using your fantastic RDKit package and very much based it on your RPC implementation there ( 😉 see the 3. Credits section). I mainly added functionality to send back and forth application states and a wrapper command for ease of use

Cursor Built to make you extraordinarily productive, Cursor is the best way to code with AI.

Haha great point ^^ your milage varies but I've found Claude sonnet 3.5 via the cursor.com integration to work reasonably well -- the copilots then pick up patterns if there's already some sensible commands within the context

For some more guidance on how to use this, Martin Buttenschön wrote a nice blogpost: www.blopig.com/blog/2024/11...

Check out our MassSpecGym dataset on @polarishq.bsky.social. 🤩

Conformational dynamics smoothen the fitness landscapes of enzymes. Who knew? 🧪🧶

Congratulations! This is very exciting news

Cradle – Cradle raises $73M Series B to Put AI-Powered Protein Engineering in Every Lab News, updates, tutorials, and more from the makers of Cradle

✨ wheeeeee we raised a series B

AI-powered automated protein optimization: matches or exceeds human performance, works without human intervention. It's pretty cool :D

(PS if you're seriously good at ML eng then we're hiring)

www.cradle.bio/blog/series-b

Amazing! Congratulations to you and the cradle team 🙌

Haha where can I order an edition of this? :D

As added bonus this allows you to use github copilot or cursor's copilot directly in pymol

Check it out here:
github.com/Croydon-Brix...

My workflow:
I use GPUs on my university's cluster to run models, etc.
When I want to look at my designs, I open a pymol session on my laptop, log into the uni vpn and send the structures to my local remote from an interactive session on the cluster.

A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.

I use it a lot for my protein design workflows together with @biotite.bsky.social.

Just `pip install pymol-remote`

Done- and hey Linna ((:

Done ✅ 🙌