iiinova — where your digital self keeps evolving

Reposted by Alex Bateman

CATH-Gene3D @cathgene3d.bsky.social · 22/08/2025

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...

eventbrite.co.uk

Protein Annotations in the age of AI

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

2127

Reposted by Alex Bateman

Aude Bernheim @audeber.bsky.social · 18/07/2025

Beyond homology: This mind blowing work demonstrates the power of genomics driven analogy for discovery in the era of structure predictions. The diversity of defense systems emerged thx to "guilt by association approaches". New analogies to uncover molecular novelties 👇. 👏 Nitzan, Rotem & al.

1214

Reposted by Alex Bateman

EMBL-EBI @ebi.embl.org · 25/06/2025

New impact case study outlines the impressive economic & scientific value of UniProt - the world-leading open data resource for protein sequence & functional information. Users save up to 219 hours per year, equivalent to net benefits of up to €5,475 per user. www.ebi.ac.uk/about/news/a...

ebi.ac.uk

Measuring the value and impact of UniProt

Case study shows the economic value and impact of UniProt, showing estimated annual gains of up to €5,475 per user.

1165

Reposted by Alex Bateman

PfamDB @pfamdb.bsky.social · 20/06/2025

🚀 HUGE NEWS: Pfam 37.4 is LIVE! 318 brand-new protein families + 4 new clans! 🧬 Total collection now: 24,736 entries! 📈 Get exploring via InterPro website, API & Pfam FTP! 💻🧪

Content
Over 24,736 entries describing protein families, domains and repeats.

0101

Reposted by Alex Bateman

Bioinformatics Advances @bioinfoadv.bsky.social · 24/03/2025

"Isopeptor" introduces a #machinelearning-based approach to systematically identify isopeptide bonds in protein models. By integrating structure-guided template matching with a logistic regression classifier, Isopeptor enhances structural annotation and model accuracy.

111

Reposted by Alex Bateman

Bioinformatics Advances @bioinfoadv.bsky.social · 24/03/2025

🧩A new article in Bioinformatics Advances: "Isopeptor: A tool for detecting intramolecular isopeptide bonds in protein structures" Read more here: doi.org/10.1093/bioadv/vbaf049

131

Reposted by Alex Bateman

EMBL-EBI @ebi.embl.org · 17/02/2025

📢 We’re looking for a new Team Leader! @enasequence.bsky.social is recruiting a Team Leader to shape the strategy and direction for the ENA and Biosamples open data resources. Interested?👇

11512

Reposted by Alex Bateman

Daniel Rigden @danielrigden.bsky.social · 27/01/2025

Well this new paper is a real pleasure! Not every Masters student gets to publish their work, so special congratulations to Olivia Pratt. www.csbj.org/article/S200... She shows that AlphaFold 2, but not other tools, has a real blind spot with perfect sequence repeats. (1/n)

csbj.org

AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins

AlphaFold 2 (AF2) has revolutionised protein structure prediction but, like any new tool, its performance on specific classes of targets, especially those potentially under-represented in its training...

2223

Reposted by Alex Bateman

Loïc Lannelongue @loiclnlg.bsky.social · 27/01/2025

🚨🌱 Interested in making scientific computing greener? Here is a chance to do just that in Cambridge: 2 open research roles to work with me and the Green Algorithms project. More details about the roles below👇 and at www.lannelongue-group.org/join/ ⏳ Closing: Feb 4 for one, Feb 17 for the other

Photo of Cambridge River and view over King's College with a group of people punting.

Photo of the Heart and Lungs Research Institute on Cambridge Biomedical Campus. The building is bronze-colour and in front of a pond.

11512

Reposted by Alex Bateman

Stephen Curry @scurry.bsky.social · 17/01/2025

Amazing - the day Steve Jobs and Tim Berners Lee ‘met’. open.substack.com/pub/stephenf...

open.substack.com

40 Years On

What We Were Like In Our Work And Our Play

043

Reposted by Alex Bateman

Bioinformatics Advances @bioinfoadv.bsky.social · 27/12/2024

🧬 "CCfrag: Scanning folding potential of coiled-coil fragments with AlphaFold" introduces a fragment-based approach to improve protein structure prediction by leveraging overlapping sequence windows for better modeling of coiled-coils. Read more: doi.org/10.1093/bioa... #ProteinFolding #AlphaFold

194

Reposted by Alex Bateman

Bioinformatics Advances @bioinfoadv.bsky.social · 19/12/2024

🔬 How does #AlphaFold2 perform with minimal sequence input? "Dissecting AlphaFold2’s capabilities with limited sequence information" reveals insights into its ability to predict #ProteinStructures using structural templates without deep MSAs. Read more: doi.org/10.1093/bioa...

072

Reposted by Alex Bateman

PfamDB @pfamdb.bsky.social · 09/12/2024

🧬 What's new in Pfam? Beta propellers uncovered through smart deduplication, fresh perspectives on haloarchaeal proteins, and more! Dive into our latest blog: xfam.wordpress.com/2024/12/09/p...

xfam.wordpress.com

Pfam 37.1 release

Pfam 37.1 release is now out and accessible through the InterPro website and Pfam ftp. More frequent Pfam updates Historically, Pfam releases occurred approximately once per year. With the de…

082

Reposted by Alex Bateman

InterPro @interprodb.bsky.social · 09/12/2024

📝 Just published: Our latest blog walks you through InterPro's major updates - from redesigned protein views to improved data exploration. Read more: proteinswebteam.github.io/interpro-blo...

051

Reposted by Alex Bateman

Bioinformatics Advances @bioinfoadv.bsky.social · 21/11/2024

ICYMI, August 2024: "Current and future directions in network biology" shares insights into advancing cellular function and disease research through #MachineLearning, multimodal data integration, and personalized medicine. Read it here: doi.org/10.1093/bioa... #NetworkBiology #SystemsBiology

152

Reposted by Alex Bateman

Tom Collins @tomcollinsresearch.bsky.social · 18/11/2024

I will start my Bluesky life by sharing an opportunity for those who are interested in researching fungi and how they adapt to their environment. Awards of up to £3 million available, more details at the link below or in our webinar on 27th November. wellcome.org/grant-fundin...

wellcome.org

Fungal adaptation | Grant Funding | Wellcome

This award will fund research on the mechanisms and triggers for fungal adaptation. Find out eligibility, what's in scope and how to apply.

043

Reposted by Alex Bateman

Izzy Jayasinghe @ijayas.bsky.social · 21/11/2024

Our friends at EMBL Australia have called for expressions of interest for the position of Scientific Head. It's a fantastic opportunity for senior scientists based in Aus to bring a vision, stakeholders, and resources to a network that has produced such vibrant scientists and discoveries. 🧪

emblaustralia.org

EMBL Australia invites expressions of interest for Scientific Head role | EMBL Australia

Professor James Whisstock is stepping down after eight transformative years as Scientific Head of EMBL Australia. Prof. Whisstock is a structural biologist at Monash Biomedicine Discovery Institute an...

24642

Reposted by Alex Bateman

ISCB News @iscb.bsky.social · 20/11/2024

🔔The ISCB November 2024 Newsletter is available! In this edition, we share new ISCB partnerships, reminders of upcoming deadlines, and information about sustainable computing in the ISCB Green Pages! 🔗 Read the newsletter here: t.ly/t8AXG

132

Alex Bateman @alexbateman1.bsky.social · 20/11/2024

I woke up in the night hearing a large rumble. Was it an earthquake? Nope, but I was surprised at how often we get little quakes in the UK! Thanks @britgeosurvey.bsky.social.

130

Alex Bateman @alexbateman1.bsky.social · 19/11/2024

Well this is interesting. Claude 3.5 Sonnet seems to have started to recognise the limits of its own understanding. This is much more useful than the usual confident sounding hallucinations we've got used to from LLMs.

261

Reposted by Alex Bateman

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 07/02/2024

302 new entries in #PDBrelease (http:/PDBe.org/latest)! Here is the structure of thioredoxin glutathione reductase from 𝑆. 𝑚𝑎𝑛𝑠𝑜𝑛𝑖, solved using X-ray crystallography (pdbe.org/8pdd). This protein acts an important target for designing new anti-schistosomal drugs.

051