OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇

This October I’m drawing one molecule a day inspired by proteins in pdb @rcsbpdb.bsky.social Day 2/31 Prompt WEAVE N-terminal domain of a Fibrion - a building block of silk fiber produced by silkworms. Pdb: 3UA0 Next prompt is CROWN and I would love your suggestions!

Viral AlphaFold Database (VAD) is live in Science Advances ~27,000 predicted viral protein monomers & homodimers Conserved folds across bacteria, archaea & eukaryotic viruses New toxin–antitoxin system KreTA uncovered Vast “functional darkness” remains uncharted www.science.org/doi/10.1126/...

Océane Follonier​ @oceanef.bsky.social for “From bytes to binders: design, score and optimize​” #bc2basel #posterprize

Critical benchmarking of structure prediction methods has been crucial for measuring progress and detecting breakthroughs. But how will the future look like? Join the discussion at our workshop in Basel on September 8 - just before the [BC]2 conference. @sib.swiss @biozentrum.unibas.ch ⬇️⬇️⬇️

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

Still some spots left, join us in Basel on Sep 8 (before [BC]2) to discuss structure prediction benchmarking and more!

🔬 Workshop: Future of Structure Prediction Benchmarking 📅 Sept 8, 2025 | Basel 💡 Talks + breakout sessions on #CASP #CAPRI #CAMEO & benchmarking for drug discovery 🎟️ Free registration (limited spots): lu.ma/ws9nu1xf Join us to explore how benchmarking can drive breakthroughs in structure prediction.

Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻 Find out about molecular modelling to systems-level analyses and evolution, and more. Submit your abstract by 26 Aug ➡️ s.embl.org/csb25-01-bl

CATH turns 30 years old this year! We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses. www.eventbrite.co.uk/e/protein-an...

AtomWorks is out! Building upon @biotite_python, we built a toolkit for all things biomolecules and trained RF3 with it. All open-source, test it via `pip install atomworks`! AtomWorks: github.com/RosettaCommo... RF3: github.com/RosettaCommo... Paper: tinyurl.com/y2w4z65b 1/6

Filtering out homologous structures from the PDB at 40% sequence identity is not enough to create a robust test set. Significant leakage persists at this level, and comparative modeling can still produce high quality models.

Looking for a #fellowship for an independent #PhD at one of the best places for life sciences in the world? The summer call at @biozentrum.unibas.ch @unibas.ch is open until October 12, 2025. www.biozentrum.unibas.ch/phd/internat...

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

The big difference is in the pairing. The MMseqs2 server pairs sequences based on species, while our old HHblits MSAs were paired based on genome proximity (number of genes apart). Working w/ @milot.bsky.social and @martinsteinegger.bsky.social we implemented the proximity filtering in server (3/4)

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

New Practical Cheminformatics Post patwalters.github.io/Three-Papers...

We will be hosting a mirror site of the CASP data and workflows at @sib.swiss. Operating a redundant site with independent funding is a good idea for important scientific infrastructure, independent from the current funding situation in the US.

Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!

Read this intro thread 🧵. CAMEO is part of SWISS-MODEL: a protein structure homology-modelling suite of software tools and databases which is one of the 17 resources in our portfolio of leading open biodata resources. @torstenschwede.bsky.social @xavier.robin.info

Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social

In this evaluation of AlphaFold3 (and other methods), we show that (i) accurate predictions are limited to RNA structures/complexes with structural similarity to PDB and (ii) that current methods are bad at estimating the accuracy of the predictions. www.biorxiv.org/content/10.1...

Check out CAMEOs flashy new website and features!

Introducing CAMEO Structures & Complexes - automated weekly blind benchmarking of structure prediction servers. Now with heteromeric and protein-ligand complexes. Join us and register your server now! cameo3d.org

We are looking for additional Group Leaders to join the growing computational biology community at VIB. If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you! https://vib.ai/en/opportunities#/job-description/110906

The final version of our work on the in-cell architecture of the mitochondrial respiratory chain is now online in @science.org 🎉 You can find the full story here www.science.org/doi/10.1126/... @verenaresch.bsky.social did a wonderful job on the cover and animation, she really brought it to life 👩‍🎨

So honoured and excited for being awarded a FWO Odysseus grant! This means, the Pereira lab will be hiring soon. Stay tuned 😃

Gemma Solomon and I are looking for a postdoc to work across the two groups on modelling biological systems with a view to applications for quantum computing More details about the project including how to apply in the link below. Deadline April 9 2025 candidate.hr-manager.net/ApplicationI...

Please spread the word! We have an opening in the Atkinson lab for a post-doc with a focus on the molecular mechanisms of microbial immune systems. Can be a fully computational or experimental or hybrid project. Read more and apply here: lu.varbi.com/en/what:job/... #phage #bioinformatics

New blog post - State of the lab 12, yearly series on being a group leader in academia. This one reflects back on the transition from junior PI to a more established scientist www.evocellnet.com/2025/03/stat...

📣 Reminder! Only two days left to submit an abstract at the [BC]² conference in one of the 6️⃣ sessions. Submissions are possible in the following 3️⃣ categories: 🔹 Oral presentation 🔹 Poster pitch 🔹 Poster 👉 Submit your abstract by Thursday 6 March: bc2.ch/talks-poster...

🚀 #AlphaFold Database update AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures. www.ebi.ac.uk/about/news/u... @pdbeurope.bsky.social

🧪🧬🔬 Postdoc in Computational Structural Biology at the @biozentrum.unibas.ch & @sib.swiss in Basel, Switzerland. www.biozentrum.unibas.ch/open-positio... The position is initially funded for 3 years, possibility to start immediately. #StructurePrediction, #Bioinformatics, #Uniprot3D, #AI

Join us in Heidelberg for the 2nd edition of #EMBOComp3D! 🧬 Explore cutting-edge AI-driven innovations and classical methods in biomolecular research, new sessions on drug design, and make contacts during the job fair. Submit your abstract by 26 Aug 👉 s.embl.org/csb25-01-bl

In case you missed it!

Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.

Watch out for an upcoming bluetorial/tweetorial on this work from the amazing @alisiafadini.bsky.social! www.biorxiv.org/content/10.1...

Excited to share what I’ve been working on with @tkaraletsos.bsky.social to transform the field of drug discovery with atomistic foundation simulation models! I could not be more thrilled to be working with this dream team. achira.ai

Some very cool stuff from the group now in paper form: “ModelArchive: a deposition database for computational macromolecular structural models” doi.org/10.1016/j.jm... And “Comparing macromolecular complexes - a fully automated benchmarking suite” doi.org/10.21203/rs.... (under review)

Reminder - this webinar is happening today at 11 AM ET! Join us live in ~40 minutes: us06web.zoom.us/webinar/regi...

Join us tomorrow to hear @peterskrinjar.bsky.social talk about 🌹 Runs N' Poses 🌹! Curious to hear your thoughts on how to keep up with benchmarking in this field.

The BioEmu-1 model and inference code are now public under MIT license!!! Please go ahead, play with it and let us know if there are issues. github.com/microsoft/bi...

@torstenschwede.bsky.social will present "Artificial intelligence - How AI is revolutionizing life science research" in German on 29 April 2025, 19:00 to 19:45 at the Maurice E. Müller room of @biozentrum.unibas.ch. 👉 www.biozentrum.unibas.ch/de/events/bi...

Check out this great BioEmu talk by @jjimenezluna.bsky.social and @yuxie.bsky.social in the VantAI lecture series. Thank you for hosting @mmbronstein.bsky.social @lucanaef.bsky.social www.youtube.com/watch?v=8vsT...

🧵 on our preprint: Zhang & Skolnick's TM score for comparing model of protein to experimental structures of same protein. The d_j are essentially the same as the aligned error in Alphafold. After any structure alignment, it's the displacement of model Calpha from experimental Calpha of residue j.

I'll post more about this later. But for a long time, we've observed odd behavior of AlphaFold's ipTM in the presence of disorder and accessory domains. Looking into the math points a way to solving the problem. There are other solutions besides ours. But I think understanding the math is key.

📢 Don’t miss the deadline ⚠️ 27 February ⚠️ to submit your abstract to the [BC]2 Basel #ComputationalBiology Conference. From #GeneExpression to #evolution or #biomedicine - we are waiting to learn more on your research projects at #bc2basel! 👉Submit your abstract now: tinyurl.com/49w6wthj

We’re hosting @peterskrinjar.bsky.social for a webinar to discuss his latest paper “Have protein co-folding methods moved beyond memorization?”! Join live on Feb 21st at 11 AM ET. Register here: us06web.zoom.us/webinar/regi... Explore Runs N’ Poses on Polaris today: polarishub.io/benchmarks/p...

RT please: Just 1.5 months away from our joint 3DBioinfo/3DSIG amazing conference! These are our two great keynote speakers! @rolanddunbrack.bsky.social & @silviaosuna.bsky.social! Check our preliminary programme here: www.iscb.org/3dbioinfo202... Registration link: www.iscb.org/3dbioinfo202...

How long does it take to predict ligand binding sites for all 220k proteins in the PDB? P2Rank 2.5 does it in 3 hours on a single CPU (16-core amd 5950x)—2x faster than the previous version 🚀. (1/n)