Awesome new tool from the Steinegger lab 🚨 A real time saver if you want to find phylogenetic variants of an RNA of interest! Check it out!

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 4d ago

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

Riboseek has now a WIP Marv Logo!

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 4d ago

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

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

Now out as a perspective in PLOS Biology. Where next for structural bioinformatics? journals.plos.org/plosbiology/...

Joe Greener@jgreener64.bsky.social · 10mo ago

I wrote a blog post about the future of structural bioinformatics. Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs? Let me know what you think. jgreener64.github.io/posts/struct...

Impressive demos. www.kimi.com/blog/kimi-k3

Excited to share our now published paper @cp-cell.bsky.social highlighting advances in modeling the evolution of protein-protein interactions with MSA Pairformer. Big thanks to Zhidian Zhang, Olivia Tang, @eunbelivable.bsky.social @milot.bsky.social @martinsteinegger.bsky.social and @sokrypton.org!

Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer

Protein language models have excelled at modeling individual proteins, but extending these capabilities to protein complexes remains a major challenge. MSA Pairformer, a parameter-efficient protein la...

cell.com

@wheelerlab.org is talking about his effort to build a resource for protein dynamics (PDB for MD). MDRepo is a repository to store simulation data. This is really needed to push the needle in design, function and more. Please help make it successful by sharing your MD data. #ismb2026 🌐 mdrepo.org

My student @yewonhan.bsky.social will talk today at 3DSIG about our work on expanding the AlphaFold database to complexes (31M predictions). It starts at 14.20 in the International Ballroom East. Please join. We also brought Marv stickers with us. #ISMB2026

@rolanddunbrack.bsky.social is talking about kinases and interface scoring (ipSAE). AF’s ipTM score avg. PAE over the full area not just the interface, so disorder and extra domains drag it down. ipSAE uses a PAE cutoff to avoid low scores, therefor only consider good interface contacts. #ismb2026

Christopher E. Mason’s keynote at the HitSeq at #ISMB2026 felt like watching an episode of „Sendung ohne Namen“ (does anybody know it?). A crazy amount of ideas, facts, and sci-fi. From environmental metagenomics to space genomics.

@yewonhan.bsky.social build a website to explore the #ISMB2026 program. Check it out here: yewon-han-bioinfo.github.io/ISMB2026-tal...

Richard Durbin starts the #ISMB2026 with his keynote about BWT for genomic search. A walk-through from BWA to his most recent work on pan-genomes GBWT. www.biorxiv.org/content/10.6.... Congratulations on the accomplishments by a Senior Scientist Award.

I’m at #ISMB2026 in Washington, DC. Please let me know if you’d like to catch up over coffee.

It seems @anthropic.com or OpenAI are unusable for biological work now. I was considering buying a Teams account, but I am worried it will be useless in the end. Has anybody experience with other LLMs?

ICML is happening in Seoul this year, and I’ve been getting several messages about lab visits. Who else will be in town and would like to meet? @milot.bsky.social lab and mine are planning a dinner on July 7th, after the reception. Let me know if you’re interested!

Just submitted my PhD thesis on algorithms for fast, large-scale k-mer-based sequence analysis. It's now available to read at phd.martayan.org Take a look and feel free to share! #Bioinformatics #PhDone

Korea reduces the immigration barriers for foreign researcher www.koreatimes.co.kr/southkorea/2... Happy to see this happening.

Korea expands ‘top-tier' visa to woo global scientists - The Korea Times

Korea is expanding its elite "top-tier" visa program to encompass foreign professors and researchers as part of an aggressive push to secure global...

koreatimes.co.kr

Why AI-assisted research might have a lower impact that some estimate? I tried to look back at the rise of the internet and its impact on scientific research as a comparison point. I should stop spending time on this but condensing this info also helps me think www.evocellnet.com/2026/06/look...

Search with TEA 🍵 Against Many! → On the web: pickybinders.org/tea/steam → Locally: github.com/PickyBinders... Feedback welcome!

Lorenzo Pantolini@lorenzopantolini.bsky.social · 8mo ago

Fresh from bioRxiv our latest work introducing The Embedded Alphabet (TEA), a powerful new representation for protein sequences obtained by discretising ESM2 embeddings into 20 characters. Pre-print: www.biorxiv.org/content/10.1... 🧵👇(1/n)

I wrote about AI in academia. "PhD-level thinking", LLM bias, grunt work, alignment, AGI, data center water use, AI politics -- something for everyone.

Thoughts on AI in academia

PhD-level thinking, LLM bias, alignment, AGI, data centers, and AI politics

open.substack.com

Does your designed active site already exist in nature? Is an uncharacterized protein hiding a catalytic site or a pocket? Folddisco answers both, searching millions of structures for a 3D motif in seconds. @natbiotech.nature.com 🧬 📄 www.nature.com/articles/s41... 🧵1/7👇

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

Folddisco enables protein structural motif search in million scale databases.

nature.com

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

Very cool! 😎⤵️ Folddisco 🪩 a motif search algorithm that supports querying both short motif queries (Fig. 1d) and long, discontinuous segments (Fig. 1e) in seconds against 53 million structures 🥳🥳 www.nature.com/articles/s41...

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

Folddisco enables protein structural motif search in million scale databases.

nature.com

Structural motif search across the protein universe with Folddisco - @martinsteinegger.bsky.social go.nature.com/4g8lCb0

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

Folddisco enables protein structural motif search in million scale databases.

go.nature.com

hetro-di-mers are released now.

EMBL-EBI@ebi.embl.org · 2mo ago

We told you it wouldn’t be a long wait. 👀 Even more predicted protein structures have been added to the #AlphaFold Database. This time, the database has expanded to include heterodimers – protein complexes made up of two different proteins. alphafold.ebi.ac.uk

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

We introduce ConforNets, a mechanism for conformational control in AlphaFold3 models - SoTA at producing diverse conformations on every multistate benchmark (N=104) - Novel capability: transfer state from one protein to another Outperforms BioEmu, ConforMix and AFsample3 🧵1/8

The CASP experiment is about to start - and is still short on challenging prediction targets. Ligand complexes, RNA, …

Torsten Schwede@torstenschwede.bsky.social · 5mo ago

Is #AI hitting a plateau in structure prediction? Help us find out at CASP17! 🧪🧬 Calling for Targets: Immune Complexes, protein - ligand complexes, RNA/DNA, conformational ensembles, membrane proteins, viral origins, and large complexes. The Rule of Thumb: If AF3 can’t model it, we want it.

10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration www.nature.com/articles/s41...

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology

FAMSA2 accurately aligns millions of protein sequences at high speed.

nature.com

(1/2) Interested in plant evolution? We are opening two PhD positions in my lab at QGG - Aarhus University, where you will combine comparative genomics and machine learning to better understand and improve crop traits. #PlantSciJobs #evolution #genomics