Alex Bateman
@alexbateman1.bsky.social
Head of Protein Sequence Resources at EMBL-EBI.
We would welcome applicants who wish to advance @pfamdb.bsky.social and/or @interprodb.bsky.social
May 21, 2025 at 8:53 AM
We would welcome applicants who wish to advance @pfamdb.bsky.social and/or @interprodb.bsky.social
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.
Still looks like a great paper.
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
academic.oup.com
May 19, 2025 at 11:26 AM
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.
Still looks like a great paper.
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...
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…
xfam.wordpress.com
April 29, 2025 at 8:32 AM
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...
I'm really excited about this InterPro release. Now including BFVD virus structures, InterPro-N matches and TED domains.
April 24, 2025 at 8:38 PM
I'm really excited about this InterPro release. Now including BFVD virus structures, InterPro-N matches and TED domains.
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.
Looks like a really useful development!
January 17, 2025 at 1:03 PM
Looks like a really useful development!
As a Claude user I found the system prompt a very interesting read.
January 2, 2025 at 9:18 AM
As a Claude user I found the system prompt a very interesting read.
You mean this photo?
January 1, 2025 at 6:01 PM
You mean this photo?
New work from the group showing that you can rescue poor quality alphafold models using AF models of homologous proteins
December 19, 2024 at 3:37 PM
New work from the group showing that you can rescue poor quality alphafold models using AF models of homologous proteins
A nice study by @atsocf.bsky.social in my lab who shows how to rescue poor quality AlphaFold models using within family templates
December 9, 2024 at 2:32 PM
A nice study by @atsocf.bsky.social in my lab who shows how to rescue poor quality AlphaFold models using within family templates