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 · 11mo ago

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

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 ...

biorxiv.org

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.

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!

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

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

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

🧵 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!

go.bsky.app/HByHiW6

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

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

🚀 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...

biorxiv.org