Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

Meet the Folddisco Marv, designed by Hyunbin Kim, who also developed Folddisco.

Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com​​​​​​​​​​​​​​​​ 🌐 https://search.foldseek.com/folddisco

Structural motif search across the protein universe with Folddisco - Nature Biotechnology

Folddisco enables protein structural motif search in million scale databases.

nature.com

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · last yr.

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

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" 😭

Theo Sanderson@theo.io · 6mo ago

I made a map of 3.4 million Bluesky users - see if you can find yourself! bluesky-map.theo.io I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail

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.

Molecular Biology and Evolution@molbioevol.bsky.social · 10mo ago

@claudele.bsky.social et al. studied the fundamental question of how enzymatic activity emerges by focusing on type B dihydrofolate reductases, suggesting DfrB domains evolved rudimentary catalysis from a binding capacity. 🔗 doi.org/10.1093/molbev/msaf215 #evobio #molbio

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

Ancient amino acid sets enable stable protein folds

Early proteins likely arose from a chemically limited set of amino acids available through prebiotic chemistry, raising a central question in molecular evolution: could such primitive compositions yie...

tinyurl.com

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

GAMA Miguel Angel@miangoar.bsky.social · 7mo ago

🧵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:

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

GAMA Miguel Angel@miangoar.bsky.social · 7mo ago

🧵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:

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

GAMA Miguel Angel@miangoar.bsky.social · 7mo ago

🧵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:

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

GAMA Miguel Angel@miangoar.bsky.social · 7mo ago

🧵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:

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...

Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years - Nature Communications

The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient microbes shaped Earth’s nitrogen cycle and offering a new experimental ...

nature.com

💪 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

GAMA Miguel Angel@miangoar.bsky.social · 7mo ago

🧵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:

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

GAMA Miguel Angel@miangoar.bsky.social · 7mo ago

🧵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:

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.

GAMA Miguel Angel@miangoar.bsky.social · 7mo ago

🧵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:

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.

GAMA Miguel Angel@miangoar.bsky.social · 7mo ago

🧵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:

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.

GAMA Miguel Angel@miangoar.bsky.social · 7mo ago

🧵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:

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.

GAMA Miguel Angel@miangoar.bsky.social · 7mo ago

🧵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:

🧵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/...

Biomedical and life science articles by female researchers spend longer under review

Women are underrepresented in academia, especially in STEMM fields, at top institutions, and in senior positions. This study analyzes millions of biomedical and life science articles, revealing that f...

journals.plos.org