Today, the AlphaFold2 paper reached the milestone of 50k citations according to Google Scholar! And AlphaFold3 will likely reach 15k citations tomorrow. Congratulations to the entire AlphaFold team, as well as to all the scientists who helped democratize protein structure prediction 🥳

Join ProSe next week Tuesday, when Noelia Ferruz @noeliaferruz.bsky.social is talking about "Controllable Protein Design with Protein Language Models and Reinforcment Learning", TUE, May 12, 5PM CET! Sign-up here: tinyurl.com/prose-seminar2

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

1/12 🧵 Do you want to learn how to design proteins using AI but don’t know anything about biology? I created a free 10-lesson course on YouTube. It’s now available in Spanish (original) and English (autodubbing w/Kokoro 82M). Here’s an overview of the topics covered in each lecture :)

AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n doi.org/10.64898/202...

I am in the "Life Sciences Super Cluster" and quite far away from many colleagues in protein design who are in the cluster called "Computational Chemistry Nexus" 😭

Does anyone know the meaning of AlphaGenome and its impact? It’s not my area, so I don’t know how important it is. But I think is not equivalent to AlphaFold2, since no other area in biology has the high-quality data and structure provided by PDB, UniProt and CASP competition.

Sometimes I see Nature papers as elegant $13k commercials from AI companies inviting you to subscribe to their chatbots

How does catalysis emerge from non-catalytic domains? In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead. A striking case of catalysis evolving from binding.

Can proteins fold and function with half of the amino acid alphabet? Using only 10 residues, we designed stable, mutation-resilient structures—no aromatics or basics involved. A minimalist foundation for ancient biology and synthetic design. tinyurl.com/37t8br4v #ProteinDesign #OriginsOfLife

I recorded ~4h where we cover the main bio databases, data processing methods, many sources of bias and topics like generalization and data leakage :) youtu.be/SKpHaHgvCKE Slides drive.google.com/file/d/1jpEwDBncJCRviG_DaWs2EpzCL_1BfB9t/view English is available only via auto-translated subtitles

I recorded ~8h introducing the main algorithms for protein design: from classical approaches to protein language models, AlphaFold, ESMFold, MPNN, diffusion models and more :) youtu.be/wKUYtAt87d4T... Slides drive.google.com/file/d/1EPLj... English is available only via auto-translated subtitles

I’ve recorded ~8h explaining the architectures of AlphaFold, AF2 & AF3, as well as the context needed to understand their development, applications and limitations :) youtu.be/_jDRr5BcTaY Slides drive.google.com/file/d/1i4QE... English is available only via auto-translated subtitles

The 7th lecture is available on YouTube :) We will review how proteins emerge and diversify throughout evolution, considering mutations and molecular interactions youtu.be/qaypRS8SX5M Slides drive.google.com/file/d/1BfQd... English is available only via auto-translated subtitles

Our new paper, out today! We resurrected ancient nitrogenases first used by life on Earth 3 billion years ago. We combined synthetic biology and geology & validated their chemical #biosignature in rocks that helps reveal ancient life on Earth!(and beyond!) Link: www.nature.com/articles/s41...

💪 NEW VIDEO: Flying over the A-band of an atomic-scale model of a vertebrate muscle sarcomere. Let's explore the molecular mechanics that make your muscles work. Rendered using @bradyajohnston.bsky.social 's molecular nodes Model based on the incredible work of the @raunser-lab.bsky.social lab

The 6th lecture is now available on YouTube :) We’ll review how proteins adopt their 3D shape, how they perform their functions and how their activity is regulated youtu.be/cZs8XtVYa5A Slides drive.google.com/file/d/1TpPj... English is available only via auto-translated subtitles

The fifth lecture of the course is now available on YouTube :) We’ll review amino acid chemistry and how we organize and classify proteins youtu.be/gE6qXwpBP_s Slides drive.google.com/file/d/1F99V... For now, the English version is only available through the automatic translation of the subtitles

The fourth lecture of the course is now available on YouTube :) We will review how Transformers and modern LLMs work youtu.be/vUpb6O6T2yQ Slides drive.google.com/file/d/1y2Vj... For now, the English version is only available through the automatic translation of the subtitles.

The third lecture of the course is now available on YouTube :) We will review how neural networks work. youtu.be/pAgL7NsCUMU Slides drive.google.com/file/d/1cazt... For now, the English version is only available through the automatic translation of the subtitles.

The second lecture of the course is now available on YouTube :) We will review what AI is, its subfields and how to train a model. youtu.be/Xx80O85-5rI Slides drive.google.com/file/d/1i-Jo... For now, the English version is only available through the automatic translation of the subtitles.

The first lecture of the course is now available on YouTube :) youtu.be/uMkZzKbnoJI Slides drive.google.com/file/d/1uDwe... For now, the English version is only available through the automatic translation of the subtitles.

🧵1/3 I created this free 37-hour course, distributed across 10 lectures, to introduce AI-based protein design. For more information about the course and its specific topics, please visit the official course page:

Cost of being female lead/corresponding author in biomedical sciences: "[T]he median amount of time spent under review is 7.4%–14.6% longer for female-authored articles than for male-authored articles" even in disciplines where women well-represented. #AcademicSky journals.plos.org/plosbiology/...

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org

www.biorxiv.org/content/10.6... most proteins are multi domain but our understanding of how architectures evolve is limited - we mapped 40K chitinases and show a stepwise “grammar” of domain gain/loss and localisation changes that predicts ecological strategy and physiological function.

I just want to create hype and say that I made a 10-class course to introduce people to AI-driven protein design. It’s around 750 slides and will be freely available for anyone who wants to use them and, most importantly, improve them. Stay tuned :)

1/2 If you think that the Protein Data Bank is a representative DB, it is not. The data is highly biased. The CATH suggests that there are 1,472 protein folds, yet among the ~600k domains present in the PDB, ~39% are represented by the 10 most abundant folds (AKA superfolds).

Thrilled to introduce TEDLH, a library of profile HMMs built from TED’s structure-derived domain annotations of the AFDB. Explore 765K HMMs capturing CATH superfamily diversity. www.biorxiv.org/content/10.6...

🕷️Spiders in your blood? Don’t worry, these are protein molecules of C4BP protein, part of your immune system. Just like real spiders, they grab prey with their “legs.” Watch them in action! Intrigued, check the paper of @tkadava.bsky.social doi.org/10.1016/j.mc... @bijvoet-centre.bsky.social

Proteins are dynamic structures, but structural biology often shows them as static snapshots. Inspired by long-exposure photography and generative art, I built ProteinCHAOS, an artistic tool inspired by molecular dynamics to capture protein flexibility over time, much like long-exposure images.

We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing: a 🧵 1/n Drain: arxiv.org/abs/2511.04820 Strain: direct.mit.edu/qss/article/... Oligopoly: direct.mit.edu/qss/article/...

I strongly recommend making cat-based diagrams to illustrate complex topics in protein science: "Figure 4 considers [...] invariance and equivariance with respect to translations and rotations in 3D. For illustration purposes, the figure includes a series of cat cartoons in 2D."

I just want to create hype and say that I made a 10-class course to introduce people to AI-driven protein design. It’s around 750 slides and will be freely available for anyone who wants to use them and, most importantly, improve them. Stay tuned :)

Happy to share Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record 🧪 It appears as part of a Special Section in @genomebiolevol.bsky.social organized by @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and J. Douglas doi.org/10.1093/gbe/...

🫡

This is a very cool ancestral reconstruction study by @krishnareddy.bsky.social et al. that I recommend reading! @rachellegaudet.bsky.social and I thought it was so interesting that we wrote a News & Views about it, check it out: rdcu.be/eCfyl

If you're an undergrad and want to intern with me, this is where you need to apply!

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...

This is a breakthrough for protein science🔥AFAIK this is the largest protein DB, with >100B seqs (3B clustered at 50%). New biology will come from LOGAN: new folds, topologies, etc. You can also improve your AlphaFold models by building better MSAs. Future AI models will also use LOGAN for training

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

1/13 🧵 Today, Bindcraft was published in @nature.com , one of the most famous AIs in biology for designing protein–protein interactions (PPI). In my opinion. Bindcraft represents one of the most important advances in the post–AlphaFold2 era.

Does anyone know of a recent comparison of the main structural classification schemes of proteins and guidance on when to choose one? Something like this but including ECOD and perhaps seq-based schemes like Pfam, SUPERFAMILY and CDD. Img source (2020) pubmed.ncbi.nlm.nih.gov/32302382/

In a new GBE Review, @cpuentelelievre.bsky.social @proteinmechanic.bsky.social & J. Douglas give an overview on protein structural phylogenetics, how to obtain evolutionary insights from structural data, and key applications and future directions. 🔗 doi.org/10.1093/gbe/evaf139 #genome #evolution

Hi @milot.bsky.social @martinsteinegger.bsky.social :) It appears that there is a problem with the FoldManson webserver. It does not allow load structures using accessions from PDB/UniProt/BFVD. e.g., when I tried with pdbID 1zg4, the error said "1 not found." The same occurs with any other acc.

Folddisco webserver result view update: - Added description texts for AFDB - Integrated TaxoView taxonomy visualization & filter by @sunjaelee.bsky.social - Inter-residue distance clustering by DBSCAN to explore motif diversity. 🌐 search.foldseek.com/folddisco 📄 www.biorxiv.org/content/10.1...

🦠🧍‍♀️From bacterial to human immunity. We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity. Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social www.science.org/doi/10.1126/...