Gabriel Axel
@gabiaxel.bsky.social
Computational protein archeologist, plant-based, cat lord
ZincSight is a novel tool for predicting zinc-binding sites. It is notably faster than similar tools, making it suitable for large-scale analysis without compromising accuracy and explainability.
📃 Paper: onlinelibrary.wiley.com/doi/10.1002/...
▶️ Notebook: colab.research.google.com/github/MECHT...
📃 Paper: onlinelibrary.wiley.com/doi/10.1002/...
▶️ Notebook: colab.research.google.com/github/MECHT...
Interpretable prediction of zinc ion location in proteins with ZincSight
Metal ions are essential for a broad range of biochemical processes in living organisms, with zinc being the second most abundant transition metal ion. Zinc has catalytic, structural, and regulatory ....
onlinelibrary.wiley.com
October 30, 2025 at 8:47 AM
ZincSight is a novel tool for predicting zinc-binding sites. It is notably faster than similar tools, making it suitable for large-scale analysis without compromising accuracy and explainability.
📃 Paper: onlinelibrary.wiley.com/doi/10.1002/...
▶️ Notebook: colab.research.google.com/github/MECHT...
📃 Paper: onlinelibrary.wiley.com/doi/10.1002/...
▶️ Notebook: colab.research.google.com/github/MECHT...
In a recent work, we demonstrate how contrastive learning of both sequence and structure reveals possible evolutionary relationships between protein domains.
📄 Preprint: www.biorxiv.org/content/10.1...
🌌 Visualization of ECOD domains distances according to CLSS: gabiaxel.github.io/clss-viewer/
📄 Preprint: www.biorxiv.org/content/10.1...
🌌 Visualization of ECOD domains distances according to CLSS: gabiaxel.github.io/clss-viewer/
October 24, 2025 at 7:29 AM
In a recent work, we demonstrate how contrastive learning of both sequence and structure reveals possible evolutionary relationships between protein domains.
📄 Preprint: www.biorxiv.org/content/10.1...
🌌 Visualization of ECOD domains distances according to CLSS: gabiaxel.github.io/clss-viewer/
📄 Preprint: www.biorxiv.org/content/10.1...
🌌 Visualization of ECOD domains distances according to CLSS: gabiaxel.github.io/clss-viewer/
Reposted by Gabriel Axel
The ProSE seminars are back after a summer break. The next speaker is Nir Ben-Tal on "Contrastive learning unites sequence and structure in a global representation of protein space".
Date: September 9
Time: 5pm CET
Register here: tinyurl.com/prose-seminar2
Please share!
🧪 #mevosky
Date: September 9
Time: 5pm CET
Register here: tinyurl.com/prose-seminar2
Please share!
🧪 #mevosky
September 2, 2025 at 1:09 PM
The ProSE seminars are back after a summer break. The next speaker is Nir Ben-Tal on "Contrastive learning unites sequence and structure in a global representation of protein space".
Date: September 9
Time: 5pm CET
Register here: tinyurl.com/prose-seminar2
Please share!
🧪 #mevosky
Date: September 9
Time: 5pm CET
Register here: tinyurl.com/prose-seminar2
Please share!
🧪 #mevosky
The Parkinson's disease mutation C212Y in Parkin E3 ubiquitin ligase RING0 domain prevents the formation of a zinc metal coordination complex, resulting in the protein misfolding, which leads to decreased mitophagy.
faseb.onlinelibrary.wiley.com/doi/10.1096/...
faseb.onlinelibrary.wiley.com/doi/10.1096/...
The Juvenile Parkinson's Disease Mutation C212Y Impairs Mitochondrial Homeostasis in a Caenorhabditis elegans Model
Only a small subset of the Parkin missense mutations have been studied. Considering the high conservation of the protein, we examined the feasibility of generating a PD disease missense mutation in C....
faseb.onlinelibrary.wiley.com
August 31, 2025 at 9:57 PM
The Parkinson's disease mutation C212Y in Parkin E3 ubiquitin ligase RING0 domain prevents the formation of a zinc metal coordination complex, resulting in the protein misfolding, which leads to decreased mitophagy.
faseb.onlinelibrary.wiley.com/doi/10.1096/...
faseb.onlinelibrary.wiley.com/doi/10.1096/...
I should post something. Here are a few tutorial videos I made for the structural biology classes I give. I hope they will be useful to someone. Feel free to suggest more topics that you would like to see in future videos. 🖥️🧬🧶 www.youtube.com/playlist?lis...
Computational Structural Biology - YouTube
www.youtube.com
November 23, 2024 at 1:30 AM
I should post something. Here are a few tutorial videos I made for the structural biology classes I give. I hope they will be useful to someone. Feel free to suggest more topics that you would like to see in future videos. 🖥️🧬🧶 www.youtube.com/playlist?lis...