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Daniel Álvarez Salmoral

@alvarezsalmoral.bsky.social
4.1K followers 501 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: alpha-bridge.eu

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Reposted by Daniel Álvarez Salmoral
Tassos Perrakis @tassosperrakis.bsky.social · 13/09/2025
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!
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Reposted by Daniel Álvarez Salmoral
Schumacher Lab @schumacher-lab.bsky.social · 02/05/2025
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...
biorxiv.org
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 ...
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Reposted by Daniel Álvarez Salmoral
Tassos Perrakis @tassosperrakis.bsky.social · 19/12/2024
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 · 19/12/2024
🎄✨ 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 · 18/12/2024
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 · 04/12/2024
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 · 03/12/2024
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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Reposted by Daniel Álvarez Salmoral
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 20/11/2024
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 · 19/11/2024
Follow our NKI community go.bsky.app/5EK1wtK
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Reposted by Daniel Álvarez Salmoral
Quanta Magazine @quantamagazine.org · 24/10/2024
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
youtu.be
How AI Solved Protein Folding and Won a Nobel Prize
YouTube video by Quanta Magazine
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Reposted by Daniel Álvarez Salmoral
Anthony Mathelier @amathelier.bsky.social · 18/11/2024
🧵 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 · 17/11/2024
⚠️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 · 18/11/2024
🚨 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...
roche.wd3.myworkdayjobs.com
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....
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Reposted by Daniel Álvarez Salmoral
Gabriele Corso @gcorso.bsky.social · 17/11/2024
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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Reposted by Daniel Álvarez Salmoral
Kate Michie @kmichie.bsky.social · 17/11/2024
go.bsky.app/HByHiW6
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Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · 17/11/2024
I haven’t come across this starter pack yet, so I made one! 👉 Check out the "Protein Prediction & Design" Starter Pack and join the conversation. Think someone should be included? Tag them below! 👇 🧬🧶 go.bsky.app/C1oNcnj
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Reposted by Daniel Álvarez Salmoral
Willie Neiswanger @willieneis.bsky.social · 10/11/2024
I'm making a list of AI for Science researchers on bluesky — let me know if I missed you / if you'd like to join! go.bsky.app/AcP9Lix
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Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · 15/11/2024
🚀 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.
biorxiv.org
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...
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