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CATH-Gene3D

@cathgene3d.bsky.social

710 followers 29 following 28 posts

CATH/Gene3D at University College London Evolutionary relationships and classification of protein domains. https://cathdb.info https://ted.cathdb.info

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Reposted by CATH-Gene3D

judewells.bsky.social @judewells.bsky.social · 20d

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.

CATH-Gene3D @cathgene3d.bsky.social · 22d

Rob Finn on MGnify, everything bacteria and functions in different environments

CATH-Gene3D @cathgene3d.bsky.social · 22d

Now Maria Martín from UniProt is telling us how AI-based tools are shaping the future of one of the key resources for protein sequences and function.

CATH-Gene3D @cathgene3d.bsky.social · 22d

From structures to sequences, now Alex Bateman and the quest to annotate and classify all proteins!

CATH-Gene3D @cathgene3d.bsky.social · 22d

Starting our afternoon session with a talk by Sameer Velankar, of PDBe and AFDB fame among other endeavours!

CATH-Gene3D @cathgene3d.bsky.social · 22d

And now @gonzaparra.bsky.social on his first talk on protein frustration as a PI! Well done!

CATH-Gene3D @cathgene3d.bsky.social · 22d

David Jones, on novel folds in AFDB and CATH’s founding being celebrated at a now-closed Pizza place in Euston Station

CATH-Gene3D @cathgene3d.bsky.social · 22d

From CATH to Computational Enzymology, Dame Janet Thornton on the birth of CATH and beyond!

CATH-Gene3D @cathgene3d.bsky.social · 22d

First Keynote by Burkhard Rost, on the impact of protein language models on the field of structural biology

CATH-Gene3D @cathgene3d.bsky.social · 22d

Kickstarting our symposium “Protein Annotations in the age of AI” at UCL!

CATH-Gene3D @cathgene3d.bsky.social · Aug 22

Congratulations @judewells.bsky.social!

RCSB Protein Data Bank @rcsbpdb.bsky.social · Aug 22

Poster Prize Awarded at ISMB/ECCB 2025
Congratulations to Jude Wells for Design in voxel space, decode in smiles space: Plixer generates drug-like molecules for protein pockets

PDB101: Poster Prize Awarded at ISMB/ECCB 2025

PDB-101: Training, Outreach, and Education portal of RCSB PDB

pdb101.rcsb.org

CATH-Gene3D @cathgene3d.bsky.social · Aug 22

If you'd like to showcase your research with a poster, details are included in the registration page.

We hope to see you there!

CATH-Gene3D @cathgene3d.bsky.social · Aug 22

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

CATH-Gene3D @cathgene3d.bsky.social · Aug 22

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-Gene3D @cathgene3d.bsky.social · Aug 22

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...

Protein Annotations in the age of AI

A not-for-profit symposium hosted at UCL - more details about speakers and venue below.

www.eventbrite.co.uk

CATH-Gene3D @cathgene3d.bsky.social · Aug 20

Another CATH outing at Greenwich Park after a lovely cruise along the Thames and a pub lunch!

Reposted by CATH-Gene3D

Nicola Bordin @nbordin.bsky.social · Apr 28

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.

Metagenomic-scale analysis of the predicted protein structure universe

Protein structure prediction breakthroughs, notably AlphaFold2 and ESMfold, have led to an unprecedented influx of computationally derived structures. The AlphaFold Protein Structure Database now prov...

www.biorxiv.org

Reposted by CATH-Gene3D

EMBL-EBI @ebi.embl.org · Mar 3

TED is a collaborative project between the structural bioinformatics groups of Professor David Jones & Professor Christine Orengo @cathgene3d.bsky.social at @ucl.ac.uk.

The TED integration is set to enhance the interpretability and usability of #AlphaFold predictions. Is this useful in your work?

Reposted by CATH-Gene3D

EMBL-EBI @ebi.embl.org · Mar 3

🚀 #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

CATH-Gene3D @cathgene3d.bsky.social · Dec 18

CATHmas lunch 2024!

CATH-Gene3D @cathgene3d.bsky.social · Nov 20

We have updated sequences in our Functional Families by scanning FunFam-HMMs against UniProt release 2024_02, giving a 276% increase in FunFams coverage. The mapping of TED structural domains has resulted in a 4-fold increase in FunFams with structural information.

CATH-Gene3D @cathgene3d.bsky.social · Nov 20

New PDB and TED data increases the number of superfamilies from 5841 to 6573, folds from 1349 to 2078 and architectures from 41 to 77.

CATH-Gene3D @cathgene3d.bsky.social · Nov 20

CATH v4.4 represents an expansion of ∼64 844 experimentally determined domain structures from PDB. We also present a mapping of ∼90 million predicted domains from TED to CATH superfamilies.

CATH-Gene3D @cathgene3d.bsky.social · Nov 20

We report a significant expansion of structural information (180-fold) for CATH superfamilies through classification of PDB domains and predicted domain structures from the Encyclopedia of Domains (TED) resource.

CATH-Gene3D @cathgene3d.bsky.social · Nov 20

A new version of CATH, v4.4, is out! 🎉

Here’s a link to the manuscript in NAR.

CATH v4.4: major expansion of CATH by experimental and predicted structural data

Abstract. CATH (https://www.cathdb.info) is a structural classification database that assigns domains to the structures in the Protein Data Bank (PDB) and

academic.oup.com