Alex Bateman
@alexbateman1.bsky.social
π€ 1281
π₯ 195
π 25
Head of Protein Sequence Resources at EMBL-EBI.
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Alex Bateman
CATH-Gene3D
3 months ago
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...
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Protein Annotations in the age of AI
A not-for-profit symposium hosted at UCL - more details about speakers and venue below.
https://www.eventbrite.co.uk/e/protein-annotations-in-the-age-of-ai-tickets-1609909214799
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Alex Bateman
Paul Gardner
3 months ago
www.nature.com/articles/s41...
From remote matches to
@rfamdb.bsky.social
models to the discovery of novel *vertebrate* riboswitches!
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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 ...
https://www.nature.com/articles/s41467-025-62815-6
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Alex Bateman
Aude Bernheim
4 months ago
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 π. π Nitzan, Rotem & al.
add a skeleton here at some point
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Alex Bateman
EMBL-EBI
5 months ago
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 β¬5,475 per user.
www.ebi.ac.uk/about/news/a...
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Measuring the value and impact of UniProt
Case study shows the economic value and impact of UniProt, showing estimated annual gains of up to β¬5,475 per user.
https://www.ebi.ac.uk/about/news/announcements/uniprot-impact-value-case-study/
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Alex Bateman
PfamDB
5 months ago
π HUGE NEWS: Pfam 37.4 is LIVE! 318 brand-new protein families + 4 new clans! 𧬠Total collection now: 24,736 entries! π Get exploring via InterPro website, API & Pfam FTP! π»π§ͺ
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Alex Bateman
Bioinformatics Advances
8 months ago
π 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:
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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...
https://github.com/FranceCosta/isopeptor
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Alex Bateman
Bioinformatics Advances
8 months ago
"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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Alex Bateman
Bioinformatics Advances
8 months ago
π§©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
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Alex Bateman
EMBL-EBI
9 months ago
π’ Weβre 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?π
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Alex Bateman
Daniel Rigden
10 months ago
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)
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AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic Ξ²-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...
https://www.csbj.org/article/S2001-0370(25)00020-0/fulltext
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Alex Bateman
LoΓ―c Lannelongue
10 months ago
π¨π± 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 belowπ and at www.lannelongue-group.org/join/ β³ Closing: Feb 4 for one, Feb 17 for the other
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Alex Bateman
Stephen Curry
10 months ago
Amazing - the day Steve Jobs and Tim Berners Lee βmetβ.
open.substack.com/pub/stephenf...
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40 Years On
What We Were Like In Our Work And Our Play
https://open.substack.com/pub/stephenfry/p/40-years-on?r=cco11&utm_medium=ios
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Alex Bateman
Bioinformatics Advances
11 months ago
𧬠"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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Alex Bateman
Bioinformatics Advances
11 months ago
π¬ How does
#AlphaFold2
perform with minimal sequence input? "Dissecting AlphaFold2βs 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
PfamDB
11 months ago
𧬠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...
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Pfam 37.1 release
Pfam 37.1 release is now out and accessible through the InterPro website and Pfam ftp.Β More frequent Pfam updates Historically, Pfam releases occurred approximately once per year. With the deβ¦
https://xfam.wordpress.com/2024/12/09/pfam-37-1-release/
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Alex Bateman
InterPro
11 months ago
π 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...
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Alex Bateman
Bioinformatics Advances
12 months ago
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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Alex Bateman
Tom Collins
12 months ago
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 Β£3 million available, more details at the link below or in our webinar on 27th November.
wellcome.org/grant-fundin...
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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.
https://wellcome.org/grant-funding/schemes/biology-fungal-adaptation
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Alex Bateman
Izzy Jayasinghe
12 months ago
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. π§ͺ
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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...
https://www.emblaustralia.org/eoi-embl-australia-scientific-head/
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Alex Bateman
ISCB News
12 months ago
πThe 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! π Read the newsletter here:
t.ly/t8AXG
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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
.
12 months ago
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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.
12 months ago
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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-...
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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
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1010/7902999?searchresult=1
12 months ago
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Alex Bateman
Protein Data Bank in Europe (PDBe)
almost 2 years ago
302 new entries in
#PDBrelease
(http:/PDBe.org/latest)! Here is the structure of thioredoxin glutathione reductase from π. ππππ πππ, solved using X-ray crystallography (
pdbe.org/8pdd
). This protein acts an important target for designing new anti-schistosomal drugs.
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