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Alex Bateman

@alexbateman1.bsky.social
1.3K followers 195 following 26 posts

Head of Protein Sequence Resources at EMBL-EBI.

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Alex Bateman @alexbateman1.bsky.social · 02/12/2025
It was a great pleasure to know and interact with Amos, he will be greatly missed.
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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.
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Paul Gardner @ppgardne.bsky.social · 19/08/2025
www.nature.com/articles/s41... From remote matches to @rfamdb.bsky.social models to the discovery of novel *vertebrate* riboswitches!
nature.com
Guanidine aptamers are present in vertebrate RNAs associated with calcium signaling and neuromuscular function - Nature Communications
150 years ago, guanidine was found to affect muscle function via unknown mechanisms. Here, Kavita et al. provide evidence that guanine-sensing RNAs are present in many eukaryotic transcripts relevant ...
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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.
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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.
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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! 💻🧪
Pfam 37.4
318 new families 
4 new clansContent
Over 24,736 entries  describing protein families, domains and repeats.
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Alex Bateman @alexbateman1.bsky.social · 21/05/2025
We would welcome applicants who wish to advance @pfamdb.bsky.social and/or @interprodb.bsky.social
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Alex Bateman @alexbateman1.bsky.social · 19/05/2025
Surprise! It folds into an Alpha-helix. Hmm, short peptides get unreasonably high pLDDT scores with AlphaFold. We see mainly alpha helix predictions for short peptides of random sequences or spurious mistranslated protein sequences: academic.oup.com/bioinformati... Still looks like a great paper.
academic.oup.com
Folding the unfoldable: using AlphaFold to explore spurious proteins
AbstractMotivation. The release of AlphaFold 2.0 has revolutionized our ability to determine protein structures from sequences. This tool also inadvertentl
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Alex Bateman @alexbateman1.bsky.social · 29/04/2025
Hi, InterPro-N is casically Pfam-N but trained across all of InterPro. So Pfam-N would be taking the InterPro-N subset that matched Pfam. Some explanation here: xfam.wordpress.com/2024/05/31/p...
xfam.wordpress.com
Pfam-N version 3: Enhancing Pfam Coverage of UniProt with Computer Vision Deep Learning Techniques
We are happy to announce the release of a new version of Pfam-N. This release is based on a new model architecture inspired by the computer vision literature, developed by Laetitia Meng-Papaxanthos…
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Alex Bateman @alexbateman1.bsky.social · 24/04/2025
I'm really excited about this InterPro release. Now including BFVD virus structures, InterPro-N matches and TED domains.
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Bioinformatics Advances @bioinfoadv.bsky.social · 24/03/2025
🔎 Isopeptor is available as a #Python-based tool that can be accessed via the command line, a Python API, or Google Colaboratory. Use it for automated isopeptide bond detection & validation in protein structures! Google Colab: t.ly/D4Lny GitHub:
github.com
GitHub - FranceCosta/isopeptor: Python package for the detection of intamolecular isopeptide bonds in protein structures.
Python package for the detection of intamolecular isopeptide bonds in protein structures. - GitHub - FranceCosta/isopeptor: Python package for the detection of intamolecular isopeptide bonds in pr...
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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.
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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
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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?👇
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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...
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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.
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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
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Alex Bateman @alexbateman1.bsky.social · 17/01/2025
Looks like a really useful development!
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Alex Bateman @alexbateman1.bsky.social · 02/01/2025
As a Claude user I found the system prompt a very interesting read.
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Alex Bateman @alexbateman1.bsky.social · 01/01/2025
You mean this photo?
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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
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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...
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Alex Bateman @alexbateman1.bsky.social · 19/12/2024
New work from the group showing that you can rescue poor quality alphafold models using AF models of homologous proteins
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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…
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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...
AI-filter in InterPro
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Alex Bateman @alexbateman1.bsky.social · 09/12/2024
A nice study by @atsocf.bsky.social in my lab who shows how to rescue poor quality AlphaFold models using within family templates
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Alex Bateman @alexbateman1.bsky.social · 30/11/2024
Very nice work. We have just added a new @pfamdb.bsky.social entry for the Pyrenoid shell proteins DiatomPyrShell PF25192. Will be available in a future Pfam release.
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Alex Bateman @alexbateman1.bsky.social · 23/11/2024
I definitely need this in my stream :-)
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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
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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.
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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...
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Alex Bateman @alexbateman1.bsky.social · 21/11/2024
Thanks. I like the new table. When I click on a node the table collapses which is good. But please add a button to uncollapse the table so I can see the complete table again.
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Alex Bateman @alexbateman1.bsky.social · 20/11/2024
Welcome to BlueSky ISCB!
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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
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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.
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Alex Bateman @alexbateman1.bsky.social · 20/11/2024
Great to see Pfam database joining the party!
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Alex Bateman @alexbateman1.bsky.social · 20/11/2024
Great to see InterPro database joining the party!
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Alex Bateman @alexbateman1.bsky.social · 20/11/2024
Well that is quite a spectacular fail ;-)
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Alex Bateman @alexbateman1.bsky.social · 19/11/2024
That is good news. Thanks
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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.
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Alex Bateman @alexbateman1.bsky.social · 18/11/2024
Actually that didn't help me. I just realised that you need to click on an edge in the network to see the interactions. I was clicking on the nodes. Can you put the info on interactions in the node pop-up?
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Alex Bateman @alexbateman1.bsky.social · 18/11/2024
Looks interesting. I have tried to find pages showing the models of PPIs with no luck. Can you make these easier to find? Perhaps have a browse page of all PPIs per virus.
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Alex Bateman @alexbateman1.bsky.social · 18/11/2024
Happy to announce that the latest UniProt NAR paper is now out. Find out what we've been up to here academic.oup.com/nar/advance-...
academic.oup.com
UniProt: the Universal Protein Knowledgebase in 2025
Abstract. The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely acce
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Alex Bateman @alexbateman1.bsky.social · 17/11/2024
Thanks Theo! This saved me a load of time :-)
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Alex Bateman @alexbateman1.bsky.social · 13/02/2024
Great series of books, now sadly out of print in the UK.
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Alex Bateman @alexbateman1.bsky.social · 13/02/2024
Already exists. See Kathryn Lasky's Guardian's of Ga'Hoole series: en.wikipedia.org/wiki/Guardia...
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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.
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