Daniel Álvarez Salmoral

Featuring #AlphaBridge features from @alvarezsalmoral.bsky.social, with @jonasteuwen.bsky.social and team, our new work from @nkinl.bsky.social nl.bsky.social @oncodeinstitute.bsky.social . Have a look at ahmpc.eu for more!

A functionally validated TCR-pMHC database for TCR specificity model development Accurate prediction of TCR specificity forms a holy grail in immunology and large language models and computational structure predictions provide a path to achieve this. Importantly, current TCR-pMHC ...

It's not the models, it's the data!

We show that a substantial proportion of a widely used TCR-pMHC database does not functionally validate, causing underestimation of performance of TCR-pMHC prediction models.

www.biorxiv.org/content/10.1...

New features in #AlphaBridge implemented by @alvarezsalmoral.bsky.social

🟥 Customisable cutoff-level for filtering on weak (0.5) or strong (0.9) interactions.
🟦 Displaying the ipTM score, and the brand-new "Contact-ipTM and #AlphaBridge scores.
🟧 Per-interface #AlphaBridge scores.

🎄✨ Early Holiday Update from AlphaBridge! ✨🎄

Exciting new features:
🔬 Confidence Filters: Identify more/less confident interfaces.
🔬 Scoring System: New scores for overall structure & individual interfaces.

Try it here!! alpha-bridge.eu 🎁

📄 Preprint: www.biorxiv.org/content/10.1...

Few years ago, our collaborators on the "base J" project identified the JBP3 protein. We had determined the crystal structure of the DNA-binding domain, but we could never make sense of the cryo-EM reconstructions of full-length JBP3: nice single particles, but AlphaFold models did not fit the maps.

Great idea!! Could you add me please?

Thrilled to present Alphabridge in the Computational Chemistry session at #NWOChains! We aim to facilitate researchers to analyze interacting interfaces in predicted biomolecular structures. Honored to share insights with top chemists in the Netherlands. 🚀🔬 Preprint: www.biorxiv.org/content/10.1...

Surely you have been using AlphaFold3 for your research project? If so, have you considered #AlphaBridge to analyze the output for macromolecule complexes prediction?

Web server: alpha-bridge.eu

Preprint: www.biorxiv.org/content/10.1...

New features coming soon!

I'd love to be added

@rborza.bsky.social should be in here for sure

My toxic trait is that I mix single and double quotes in Python

Follow our NKI community go.bsky.app/5EK1wtK

How AI Solved Protein Folding and Won a Nobel Prize YouTube video by Quanta Magazine

An AI breakthrough recently solved one of the hardest puzzles in biology and won three researchers the 2024 Nobel Prize in Chemistry. Now, on our YouTube channel, watch our short documentary to learn how this science came together: youtu.be/cx7l9ZGFZkw

Can you add us @rborza.bsky.social and me please??

Illustration comparing the improvement process in software writing to rock climbing.

🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices.

In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.

academic.oup.com/bioinformati...

⚠️THREAD OF ALL SCIENCE-RELATED STARTER PACKS! ⚠️

🔄Share to help people finding its topic/field

- STRUCTURAL BIOLOGY

Structural Biology 1: bsky.app/starter-pack...
Structural Biology 2: bsky.app/starter-pack...
Crystallography: bsky.app/starter-pack...
Synchrotron&CryoEM: bsky.app/starter-pack...

🚨 Attention #teamtomo PhD students! 🚨 12-week paid internship opportunity at Genentech. Want to see how we use cryoET in pharma? And spend the summer 2025 in the Bay Area? Details and application link here: roche.wd3.myworkdayjobs.com/ROG-A2O-GENE...

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!

Hi!! Could you add me please??

Hi!! Can you include me in this one??

Id love to join!!

I'd love to join as well!!

Hi!! Me and @rborza.bsky.social would love to be added!!

Great idea!! I'd love to join!!!

I'd love to join!!

Hi!! I would love to be added as well!!

I'd love to join!!

No he estado en un red social mas activo que aqui, es increíble

omg of course!!! Thanks for letting me know!!

Not at all, I Just did!!