iiinova — where your digital self keeps evolving

Reposted by Simon Mathis

Chaitanya K. Joshi @chaitjo.bsky.social · 15/08/2025

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...

05418

Reposted by Simon Mathis

Tomáš Pluskal @pluskal-lab.org · 24/05/2025

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.

05220

Simon Mathis @simonmathis.bsky.social · 10/05/2025

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

030

Reposted by Simon Mathis

briantrippe.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 Mathis

Adrian 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 Mathis

Gabriele Corso @gcorso.bsky.social · 08/12/2024

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

23011

Reposted by Simon Mathis

owl @owlposting1.bsky.social · 04/12/2024

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

owlposting.com

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

2.1 hours listening time

15614

Reposted by Simon Mathis

Philippe Schwaller @pschwllr.bsky.social · 02/12/2024

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

610271

Simon Mathis @simonmathis.bsky.social · 29/11/2024

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

blopig.com

Controlling PyMol from afar | Oxford Protein Informatics Group

1184

Reposted by Simon Mathis

Roman Bushuiev @roman-bushuiev.bsky.social · 27/11/2024

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

0103

Reposted by Simon Mathis

Diego del Alamo @delalamo.xyz · 27/11/2024

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

Another important biophysical factor underlying how fitness landscapes are traversed during evolution is conformational sampling, i.e. the ability of proteins to adopt multiple conformational substates.48,49 Different conformational substates could have different activities and thus contribute differently to the net fitness of the protein: conformation “A” could represent 5% of the populated states, but catalyze a new reaction that the other conformations cannot. Evolution can then act to smoothly “tune” the function of the protein through remote mutations that shift its conformational equilibrium by relatively stabilizing conformation “A”. This results in a smoother landscape because there are generally many more pathways by which a pre-existing conformational equilibrium between two conformations can be affected by remote mutations than the number of solutions that are available through complete remodeling of an active site. For example, the laboratory evolution of phosphotriesterase into an into arylesterase was tracked with protein crystallography, which revealed that almost all the mutations were remote from the active site and shifted the conformational equilibrium to favor pre-existing states that were beneficial to the new catalytic activity (50). The same process was observed in the evolution of a computationally designed Kemp eliminase, wherein gradual changes in the conformational sampling between inactive and active states resulting in a remarkably smooth evolutionary transition (51). These examples of evolutionary trajectories generated by laboratory evolution demonstrate how conformational flexibility can produce smooth fitness landscapes, and help explain the high frequency of remote mutations observed in evolutionary trajectories (52).

2316

Reposted by Simon Mathis

Patrick 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-b

cradle.bio

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

2813

Simon Mathis @simonmathis.bsky.social · 25/11/2024

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`

44713

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