Simon Mathis @simonmathis.bsky.social · 16/01/2026Super cool work - congratulations @umbislupo.bsky.social & team! 020
Reposted by Simon MathisNate Corley @ncorley.bsky.social · 15/08/2025(1/7) 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) [www.biorxiv.org/content/10.1101/202…...)biorxiv.orgAccelerating Biomolecular Modeling with AtomWorks and RF3Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita... 26728
Reposted by Simon MathisChaitanya K. Joshi @chaitjo.bsky.social · 15/08/2025RosettaFold 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... 05418
Reposted by Simon MathisTomáš Pluskal @pluskal-lab.org · 24/05/2025This 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. 05220
Simon Mathis @simonmathis.bsky.social · 10/05/2025Very nice, thoughtful post - I really enjoyed the read @pascalnotin.bsky.social 030
Reposted by Simon Mathisbriantrippe.bsky.social @briantrippe.bsky.social · 19/02/2025🔥 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 ⬇️ 14117
Reposted by Simon MathisAdrian Bunzel @bunzela.bsky.social · 12/02/2025🚨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/🧵 1307
Reposted by Simon MathisGabriele Corso @gcorso.bsky.social · 08/12/2024You 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 23011
Reposted by Simon Mathisowl @owlposting1.bsky.social · 04/12/2024Can 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 scienceowlposting.comCan AI improve the current state of molecular simulation? (Corin & Ari Wagen, Ep #1)2.1 hours listening time 15614
Simon Mathis @simonmathis.bsky.social · 04/12/2024Thank you for the feedback! That’s great to hear 🙌 010
Simon Mathis @simonmathis.bsky.social · 02/12/2024(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 000
Simon Mathis @simonmathis.bsky.social · 02/12/2024(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 ... 100
Reposted by Simon MathisPhilippe Schwaller @pschwllr.bsky.social · 02/12/2024We 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 610271
Simon Mathis @simonmathis.bsky.social · 30/11/2024Thank 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 100
Simon Mathis @simonmathis.bsky.social · 30/11/2024Haha 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 contextcursor.comCursorBuilt to make you extraordinarily productive, Cursor is the best way to code with AI. 110
Simon Mathis @simonmathis.bsky.social · 29/11/2024For some more guidance on how to use this, Martin Buttenschön wrote a nice blogpost: www.blopig.com/blog/2024/11...blopig.comControlling PyMol from afar | Oxford Protein Informatics Group 1184
Reposted by Simon MathisRoman Bushuiev @roman-bushuiev.bsky.social · 27/11/2024Check out our MassSpecGym dataset on @polarishq.bsky.social. 🤩 0103
Reposted by Simon MathisDiego del Alamo @delalamo.xyz · 27/11/2024Conformational dynamics smoothen the fitness landscapes of enzymes. Who knew? 🧪🧶 2316
Reposted by Simon MathisPatrick Kidger @patrickkidger.bsky.social · 26/11/2024✨ 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-bcradle.bioCradle – Cradle raises $73M Series B to Put AI-Powered Protein Engineering in Every LabNews, updates, tutorials, and more from the makers of Cradle 2813
Simon Mathis @simonmathis.bsky.social · 26/11/2024Amazing! Congratulations to you and the cradle team 🙌 010
Simon Mathis @simonmathis.bsky.social · 25/11/2024As added bonus this allows you to use github copilot or cursor's copilot directly in pymol 100
Simon Mathis @simonmathis.bsky.social · 25/11/2024Check it out here: github.com/Croydon-Brix...github.comGitHub - Croydon-Brixton/pymol-remote: Send data to and from pymol from a remote server (e.g. a cluster running deep learning workflows)Send data to and from pymol from a remote server (e.g. a cluster running deep learning workflows) - Croydon-Brixton/pymol-remote 000
Simon Mathis @simonmathis.bsky.social · 25/11/2024My 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. 110
Simon Mathis @simonmathis.bsky.social · 25/11/2024A 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` 44713
Simon Mathis @simonmathis.bsky.social · 21/11/2024@chaitjo.bsky.social this looks of interest to you 010
Simon Mathis @simonmathis.bsky.social · 21/11/2024Good to see you here, Sagardip -- I've added you! Thank you for reaching out 000
Simon Mathis @simonmathis.bsky.social · 21/11/2024Any chance you could add an 'enzymes' tag to the list? Would be curious to see how that landscape there looks like -- off the top of my head e.g. basecamp research, allozymes, cradle, xyme.ai, LIGO, birch biosciences ( @milesgander.bsky.social ), zymvol ... would fall under that tag 130
Simon Mathis @simonmathis.bsky.social · 21/11/2024Nice overview, thank you @harrisbio.bsky.social ! 010
Simon Mathis @simonmathis.bsky.social · 20/11/2024Thanks for sharing @tomsilico.bsky.social -- are you aware of a group on quantum chemistry on 🦋 by any chance? Would love to connect that community with the AI x Enzyme crowd 100
Simon Mathis @simonmathis.bsky.social · 20/11/2024Just realized ppl can only DM if we're mutual followers -- feel free to just drop a message in this feed instead then (whilst I figure out if there's a way to open up my DMs here) 100
Simon Mathis @simonmathis.bsky.social · 20/11/2024Wow cool, I just saw that it even auto-generates a feed for the people included in the list 👀 000
Simon Mathis @simonmathis.bsky.social · 20/11/2024Also let me know if there's anyone else on 🦋 whom I should add 100
Simon Mathis @simonmathis.bsky.social · 20/11/2024🧪 For people interested in AI & enzymes (enzyme engineering, design, discovery, ...), I'm assembling a starter pack for us. DM if you'd like to be included! go.bsky.app/MhfaQBh 6368
Simon Mathis @simonmathis.bsky.social · 20/11/2024Thank you for organising this @kevinkaichuang.bsky.social 020