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Daniel Álvarez Salmoral

@alvarezsalmoral.bsky.social

4K followers 500 following 33 posts

PhD Candidate at @NKI_nl in Structural Bioinformatics - Cancer Research | Perrakis lab | Interest in AI | Computational Biology, Statistics, Protein Prediction & Design 🖥️🧬 AlphaBridge web server: https://alpha-bridge.eu/

alpha-bridge.eu

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Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 15

🚀 Excited to share my first preprint on bioRxiv

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

AlphaBridge simplifies protein structure predictions for experts and novices by combining complex analysis with visual representations and interactive tools in one user-friendly platform.

AlphaBridge: tools for the analysis of predicted macromolecular complexes

Artificial intelligence (AI)-powered protein structure prediction methods have revolutionised how life scientists explore macromolecular function. Using AI to predict the structure of macromolecular c...

www.biorxiv.org

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Reposted by Daniel Álvarez Salmoral

Tassos Perrakis @tassosperrakis.bsky.social · 25d

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!

bioRxivpreprint @biorxivpreprint.bsky.social · 26d

Integrating computational protein structure predictions and genetic dependencies yields an atlas of human multi-protein complexes (AHMPC) https://www.biorxiv.org/content/10.1101/2025.09.09.675133v1

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Reposted by Daniel Álvarez Salmoral

Schumacher Lab @schumacher-lab.bsky.social · May 2

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...

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 ...

www.biorxiv.org

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Reposted by Daniel Álvarez Salmoral

Tassos Perrakis @tassosperrakis.bsky.social · Dec 19

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.

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Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Dec 19

🎄✨ 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...

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Reposted by Daniel Álvarez Salmoral

Tassos Perrakis @tassosperrakis.bsky.social · Dec 18

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.

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Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Dec 6

Great idea!! Could you add me please?

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Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Dec 4

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...

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Reposted by Daniel Álvarez Salmoral

Tassos Perrakis @tassosperrakis.bsky.social · Dec 3

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!

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Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 25

I'd love to be added

Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 24

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

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Reposted by Daniel Álvarez Salmoral

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Nov 20

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

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Reposted by Daniel Álvarez Salmoral

Netherlands Cancer Institute @nkinl.bsky.social · Nov 19

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

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Reposted by Daniel Álvarez Salmoral

Quanta Magazine @quantamagazine.bsky.social · Oct 24

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

How AI Solved Protein Folding and Won a Nobel Prize

YouTube video by Quanta Magazine

youtu.be

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Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 18

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

Reposted by Daniel Álvarez Salmoral

Anthony Mathelier @amathelier.bsky.social · Nov 18

🧵 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...

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

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Reposted by Daniel Álvarez Salmoral

Razvan Borza @rborza.bsky.social · Nov 17

⚠️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...

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Reposted by Daniel Álvarez Salmoral

Alexis Rohou @alexisrohou.bsky.social · Nov 18

🚨 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...

2025 Summer Intern - Department of Structural Biology

Department Summary The CryoEM Group in the Department of Structural Biology is dedicated to providing high-resolution structural insights into biological macromolecules involved in health and disease....

roche.wd3.myworkdayjobs.com

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Reposted by Daniel Álvarez Salmoral

Gabriele Corso @gcorso.bsky.social · Nov 17

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!

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Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 17

Hi!! Could you add me please??

Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 17

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

Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 17

Id love to join!!

Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 17

I'd love to join as well!!

Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 17

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

Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 17

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

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Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 17

I'd love to join!!