Simon Mathis
@simonmathis.bsky.social
PhD student at Uni of Cambridge, UK 🔬 | AI for protein design & engineering 🧬 | biotech & environmental applications 🌱 | enzymes 🏗️ 🇦🇹🇨🇭
Congratulations @chaitjo.bsky.social ! 🙌
Chaitanya K. Joshi@chaitjo.bsky.social · 8mo agoIntroducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀 📝: tinyurl.com/gRNAde-paper Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
(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) [https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
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...
biorxiv.org
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.
Nature Biotechnology@natbiotech.nature.com · last yr.Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - @pluskal-lab.org @iocbprague.bsky.social go.nature.com/4k1n5iC
Very nice, thoughtful post - I really enjoyed the read @pascalnotin.bsky.social
Pascal Notin@pascalnotin.bsky.social · last yr.Even simple methods leveraging these 2 modalities significantly outperform billion-parameter sequence-only models. So, what's next? Better retrieval, advanced multimodal approaches, & alignment. Read more: pascalnotin.substack.com/p/have-we-hi... #BioTech #AI #pLMs
🔥 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/🧵
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? 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
Can AI improve the current state of molecular simulation? (Corin & Ari Wagen, Ep #1)
2.1 hours listening time
owlposting.com
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
For some more guidance on how to use this, Martin Buttenschön wrote a nice blogpost: www.blopig.com/blog/2024/11...
Controlling PyMol from afar | Oxford Protein Informatics Group
blopig.com
Simon Mathis@simonmathis.bsky.social · 2y agoA 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`
Check out our MassSpecGym dataset on @polarishq.bsky.social. 🤩
Cas@caswognum.nl · 2y agoWow! 🤩 This may be the most carefully documented dataset on @polarishq.bsky.social. Great work by @roman-bushuiev.bsky.social! Do I have any #MassSpec researchers in my 🦋 network yet? I would love to hear what you think! github.com/polaris-hub/... #mass #spectrometry #dataset #benchmark
Conformational dynamics smoothen the fitness landscapes of enzymes. Who knew? 🧪🧶
Colin Jackson@cjjackson.bsky.social · 2y agodealing with the ruggedness of protein fitness landscapes is perhaps the most challenging aspect of protein design and engineering - here we have written a short perspective about it - it's complicated and not perfectly understood but very interesting! arxiv.org/abs/2411.12957
✨ 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
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
cradle.bio
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`
Nice overview, thank you @harrisbio.bsky.social !
Charlie Harris@harrisbio.bsky.social · 2y agoNow I can share external links without the posts being down regulated - I thought it would share this again!:) I have compiled a list of now 100+ companies in the 'TechBio' space into a fully open database for the community. Find here and please share if you like open.substack.com/pub/harrisbi...
🧪 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
