Alex Bateman
@alexbateman1.bsky.social
Head of Protein Sequence Resources at EMBL-EBI.
Reposted by Alex Bateman
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...
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
August 22, 2025 at 10:45 AM
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...
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...
Reposted by Alex Bateman
www.nature.com/articles/s41... From remote matches to @rfamdb.bsky.social models to the discovery of novel *vertebrate* riboswitches!
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 ...
www.nature.com
August 19, 2025 at 1:20 AM
www.nature.com/articles/s41... From remote matches to @rfamdb.bsky.social models to the discovery of novel *vertebrate* riboswitches!
Reposted by Alex Bateman
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.
The diversity of defense systems emerged thx to "guilt by association approaches". New analogies to uncover molecular novelties 👇.
👏 Nitzan, Rotem & al.
📢Preprint out!
Excited to share my final work from the @soreklab.bsky.social!
We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery.
Found 3 new families targeting immune signaling!
Excited to share my final work from the @soreklab.bsky.social!
We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery.
Found 3 new families targeting immune signaling!
July 18, 2025 at 7:08 AM
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.
The diversity of defense systems emerged thx to "guilt by association approaches". New analogies to uncover molecular novelties 👇.
👏 Nitzan, Rotem & al.
Reposted by Alex Bateman
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...
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...
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.
www.ebi.ac.uk
June 25, 2025 at 3:24 PM
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...
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...
Reposted by Alex Bateman
🚀 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!
💻🧪
318 brand-new protein families + 4 new clans! 🧬
Total collection now: 24,736 entries! 📈
Get exploring via InterPro website, API & Pfam FTP!
💻🧪
June 20, 2025 at 8:47 AM
🚀 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!
💻🧪
318 brand-new protein families + 4 new clans! 🧬
Total collection now: 24,736 entries! 📈
Get exploring via InterPro website, API & Pfam FTP!
💻🧪
Reposted by Alex Bateman
🔎 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: https://t.ly/D4Lny
GitHub:
Google Colab: https://t.ly/D4Lny
GitHub:
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...
github.com
March 24, 2025 at 12:02 PM
🔎 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: https://t.ly/D4Lny
GitHub:
Google Colab: https://t.ly/D4Lny
GitHub:
Reposted by Alex Bateman
"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.
March 24, 2025 at 12:02 PM
"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.
Reposted by Alex Bateman
🧩A new article in Bioinformatics Advances: "Isopeptor: A tool for detecting intramolecular isopeptide bonds in protein structures"
Read more here: https://doi.org/10.1093/bioadv/vbaf049
Read more here: https://doi.org/10.1093/bioadv/vbaf049
March 24, 2025 at 12:02 PM
🧩A new article in Bioinformatics Advances: "Isopeptor: A tool for detecting intramolecular isopeptide bonds in protein structures"
Read more here: https://doi.org/10.1093/bioadv/vbaf049
Read more here: https://doi.org/10.1093/bioadv/vbaf049
Reposted by Alex Bateman
📢 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?👇
@enasequence.bsky.social is recruiting a Team Leader to shape the strategy and direction for the ENA and Biosamples open data resources.
Interested?👇
February 17, 2025 at 11:07 AM
📢 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?👇
@enasequence.bsky.social is recruiting a Team Leader to shape the strategy and direction for the ENA and Biosamples open data resources.
Interested?👇
Reposted by Alex Bateman
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)
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)
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...
www.csbj.org
January 27, 2025 at 10:52 AM
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)
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)
Reposted by Alex Bateman
🚨🌱 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
More details about the roles below👇 and at www.lannelongue-group.org/join/
⏳ Closing: Feb 4 for one, Feb 17 for the other
January 27, 2025 at 12:52 PM
🚨🌱 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
More details about the roles below👇 and at www.lannelongue-group.org/join/
⏳ Closing: Feb 4 for one, Feb 17 for the other
Reposted by Alex Bateman
Amazing - the day Steve Jobs and Tim Berners Lee ‘met’. open.substack.com/pub/stephenf...
40 Years On
What We Were Like In Our Work And Our Play
open.substack.com
January 17, 2025 at 2:47 PM
Amazing - the day Steve Jobs and Tim Berners Lee ‘met’. open.substack.com/pub/stephenf...
Reposted by Alex Bateman
🧬 "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
Read more: doi.org/10.1093/bioa... #ProteinFolding #AlphaFold
December 27, 2024 at 3:03 PM
🧬 "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
Read more: doi.org/10.1093/bioa... #ProteinFolding #AlphaFold
Reposted by Alex Bateman
🔬 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...
"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...
December 19, 2024 at 2:40 PM
🔬 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...
"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...
Reposted by Alex Bateman
🧬 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...
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…
xfam.wordpress.com
December 9, 2024 at 9:58 AM
🧬 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...
Reposted by Alex Bateman
📝 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...
December 9, 2024 at 10:06 AM
📝 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...
Reposted by Alex Bateman
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
Read it here: doi.org/10.1093/bioa...
#NetworkBiology #SystemsBiology
November 21, 2024 at 5:21 PM
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
Read it here: doi.org/10.1093/bioa...
#NetworkBiology #SystemsBiology
Reposted by Alex Bateman
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/grant-fundin...
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.
wellcome.org
November 18, 2024 at 2:49 PM
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/grant-fundin...
Reposted by Alex Bateman
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. 🧪
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...
www.emblaustralia.org
November 21, 2024 at 7:38 AM
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. 🧪
Reposted by Alex Bateman
🔔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
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
November 20, 2024 at 2:55 PM
🔔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
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
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.
November 20, 2024 at 11:21 AM
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.
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.
November 19, 2024 at 8:45 PM
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.
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-...
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
academic.oup.com
November 18, 2024 at 9:47 AM
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-...
Reposted by Alex Bateman
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.
February 7, 2024 at 10:00 AM
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.