Had a great time at the #ML4NGP Training school in Sevilla! Back to Italy tomorrow (normally it would be back to London but things change!) P.S. Signed my TT contract with @unipd.bsky.social , starting March 23rd. Exciting!

To advance the family-based modelling approach, we are releasing the entire framework open source: ProFam Atlas: A curated, large-scale training corpus containing nearly 40 million protein families. Code & Weights: github.com/alex-hh/prof... Data: zenodo.org/records/1771...

For design, ProFam-1 excels at homology-guided generation. It produces diverse sequences with low sequence identity to natural proteins while preserving predicted structural similarity and conservation patterns of the natural family, even when conditioning on just a single example sequence.

Built by CATH, TÜM and NVIDIA, ProFam-1 is our new open-source protein family language model (pfLM) designed to generate functional protein variants and predict fitness using in-context example sequences.

Going full circle! 😊 The University of Padua was home for both my Bachelor’s and Master’s degrees. After 7 amazing years at UCL in the Orengo Group, I’m really happy to share that I’ve won a Tenure-Track Assistant Professorship in Biochemistry at my Alma Mater!

From Sameer Velankar & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #AlphaFold #Protein #Structure #Database 2025: a redesigned interface and updated structural coverage | #Bioinformatics #Proteomics #OpenScience #AFDB 🧪🔓 CC/ @ebi.embl.org ⬇️ academic.oup.com/nar/advance-...

We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated. mrc.tal.net/vx/appcentre...

It was lovely to speak at the CATH 30 symposium, celebrating 30 years of the @cathgene3d.bsky.social protein structure classification database. I was presenting recent work on our new generative protein-family language model: preprint coming soon.

Packing for our first flight with our kid tomorrow. Wish us luck! We went from 9kg of checked luggage for 2 months in Thailand to 3 checked suitcases and a pram. Send help!

We have a stellar lineup of speakers! Christine Orengo Burkhard Rost Janet Thornton David Jones Gonzalo Parra @gonzaparra.bsky.social Sameer Velankar Alex Bateman Maria Martin Rob Finn Gerardo Tauriello Alexey Murzin

There will be talks from world leaders in structural bioinfomatics on various themes including pioneering protein language models and key international resources including: PDBe, InterPro, UniProt, MGnify, SWISS-MODEL, FrustraEvo and CATH.

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...

Today I became a British citizen! 🇬🇧

#ISMBECCB2025 is over! Back to London tomorrow after a science feast, a talk, and a selfie with John Jumper. Not too bad!

Today at 2 PM at 3DSIG #ISMBECCB2025, @nbordin.bsky.social presents our joint work on metagenomic-scale clustering and novel domain discovery in predicted structures! 📄 www.biorxiv.org/content/10.1... Also check out poster: B-50 lolalign Sensitive structural alignments by Lasse B-123 BFVD by Rachel

Off to Liverpool for #ISMBECCB2025! Looking forward to some awesome science and friends!

"in 2025 we will have flying cars" 😂😂😂

We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments. 🌐 afesm.foldseek.com Read more about the work in the skeetorial 🦋 bsky.app/profile/mart... or our preprint 📄 www.biorxiv.org/content/10.1...

Our latest preprint is out on bioRxiv! A collaboration between the groups of @martinsteinegger.bsky.social , David Jones and Christine Orengo, we clustered AlphaFold Database and ESMatlas, a whopping 821 million proteins! We reveal biome-specific groups & over 11k novel domain combinations.

I dropped off the radar for a bit, as Aria, our daughter, was born two months earlier than expected! My wife was discharged from the hospital a week later after being stabilised. Aria has spent the last 40 days in the Neonatal Unit at Hillingdon Hospital, with wonderful care from the NHS.

See you in Liverpool at ISMB/ECCB 2025!

First time sitting on the “attack” end of a PhD viva! Really enjoyed the experience!

AlphaFold DB now has TED integrated! This is a special one for me — my first project where I took ownership from start to finish, bringing together different teams to integrate domain annotations into #AlphaFold DB. A huge learning experience, and I’m excited to finally see it live! 🧵(1/6)

🚀 #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

Excited to share PoET-2, our next breakthrough in protein language modeling. It represents a fundamental shift in how AI learns from evolutionary sequences. 🧵 1/13

Just booked flights and accommodation for the ML4NGP symposium followed by 3DBioinfo in Barcelona in March! Looking forward to see friends and collaborators! Straight to Italy for sitting on a PhD viva panel, busy weeks!

Foldseek 10 with 4-27x (1-8 GPUs) faster search through MMseqs2-GPU. Faster ProstT5 protein search w/o structure prediction through multi-GPU/Apple Metal, new BFVD/BFMD databases and multimer clustering (preview). 💾 github.com/steineggerla... 📄 www.biorxiv.org/content/10.1... 🐍 available in bioconda

A really good day! Submitted a grant/TT proposal, finished reviewing a PhD thesis and wrapping up the last chapters of Shogun!

We are excited to announce the 1st webinar from this year on January 20th! This time we will have a full lecture by Prof. David Jones from UCL presenting their recent publication in ScienceMagazine: www.science.org/doi/abs/10.1... Register here: elixir-europe.org/events/3d-bi...

Closed the accounts on the other place!

CATHmas lunch 2024!

Had a blast in Sevilla for the viva of a colleague, really looking forward to be back next year at the tribunal table :)

Back to Sevilla for a viva! Very emotional, my flat was in this square, and I loved living there during my PhD ❤️

After two years, our paper on generative models for structure-based drug design is finally out in @natcomputsci.bsky.social www.nature.com/articles/s43...

🔴El BSC contará con dos nuevos investigadores Ramón y Cajal #RyC 🌟Son @gonzaparra.bsky.social y @afcastr0t.bsky.social Las ayudas Ramon y Cajal reconocen trayectorias científicas destacadas y promueven la estabilización de personal científico excelente 💫Enhorabuena!

With great pleasure we host today Christine Orengo @uclofficial.bsky.social at @bsc-cns.bsky.social talking about the CATH protein/domain universe and what it tells us about function (mapping seq info to structures at large scale).

I’ve started working on this project towards the end of my PhD, good to see it out after 6 years! We did a genome-wide comparison of PVC bacteria living in the depth of the oceans. So much undiscovered biology there! doi.org/10.1007/s104...

Today we had the pleasure of listening to a great talk by @gonzaparra.bsky.social at UCL!

Gave a lecture in the same hall where I graduated at the University of Padova, and got to trek up to my mountains!

‘A place of joy’: why scientists are joining the rush to Bluesky For me, it certainly feels good to be here! @natureportfolio.bsky.social @bsky.app www.nature.com/articles/d41...

A new CATH release is out! 🎉

Hi TED! 👋 Out now in Science, we are finally ready to make our classification of all domains in AFDB v4 available to all! A joint effort of @cathgene3d.bsky.social and the Jones group (PSIPRED), here's a link to the article www.science.org/doi/10.1126/... 1/6 🧵⤵️

GPU-accelerated homology search with MMseqs2 https://www.biorxiv.org/content/10.1101/2024.11.13.623350v1

Hello 🦋! We are CATH! We classify protein domains in homologous superfamilies from the Protein Data Bank and AlphaFold Database! Follow us for our latest research!

Passed unanimously the “Abilitazione Scientifica Nazionale” by the Italian Government! 🇮🇹 Officially a scientist! 😁

After an intense two-days with the Rost group and NVIDIA visiting us at UCL, back to Darwin today to catch up with everything else!

Slowly moving to Bluesky! Thinking of opening a sister #CATH account here as well!

Happy New Year everyone! Feels strange being back to the UK after two months out for remote work and honeymoon! A big year ahead.. lots of changes in the making!

I’m pretty new here. Any advice?