Lightnews — Scholar-powered news

Reposted by Diego Javier Zea

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Jul 7

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco

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Diego Javier Zea @diegozea.bsky.social · Jun 24

📢 Deadline Extended!
The application deadline for the PhD student position has been extended to July 4th. If you haven’t applied yet, there’s still time! 👇

Diego Javier Zea @diegozea.bsky.social · Jun 12

Great news! I’m hiring a PhD student in structural #Bioinformatics to work on modeling protein conformations and interactions at @i2bcparissaclay.bsky.social
as part of the ANR SPPICES project! 🚀

📅 Start: 1 Sept 2025
⏳ Deadline: 23 June 2025
👉Apply now: emploi.cnrs.fr/Offres/Docto...

Portail Emploi CNRS - Offre d'emploi - Doctorant en bioinformatique structurale et évolution des protéines (H/F)

emploi.cnrs.fr

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Diego Javier Zea @diegozea.bsky.social · Jun 13

Join the MAGI team at @i2bcparissaclay.bsky.social as part of the ANR SPPICES project 🌶️
This position involves collaboration with members of the ML4NGP network on machine learning & non-globular proteins
Learn more 👉 sppices.notion.site

ANR SPPICES

Scoring and Predicting Protein Interactions and Conformations based on Evolutionary Signals

sppices.notion.site

Diego Javier Zea @diegozea.bsky.social · Jun 13

🚨 We're hiring a Bioinformatics Engineer!
🛠️ Develop #JuliaLang & Python tools to model structural and evolutionary features of IDPs
📅 Start: 1 Sept 2025
🎓 3+ years of higher education (Master’s or engineering diploma preferred)
👉 Apply now: emploi.cnrs.fr/Offres/CDD/U...

Portail Emploi CNRS - Offre d'emploi - Ingénieur bioinformaticien – Analyse computationnelle des protéines intrinsèquement désordonnées (H/F)

emploi.cnrs.fr

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Diego Javier Zea @diegozea.bsky.social · Jun 12

Learn more about the SPPICES project (Scoring and Predicting Protein Interactions and Conformations based on Evolutionary Signals) here:
sppices.notion.site

ANR SPPICES

Scoring and Predicting Protein Interactions and Conformations based on Evolutionary Signals

sppices.notion.site

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Diego Javier Zea @diegozea.bsky.social · Jun 12

Great news! I’m hiring a PhD student in structural #Bioinformatics to work on modeling protein conformations and interactions at @i2bcparissaclay.bsky.social
as part of the ANR SPPICES project! 🚀

📅 Start: 1 Sept 2025
⏳ Deadline: 23 June 2025
👉Apply now: emploi.cnrs.fr/Offres/Docto...

Portail Emploi CNRS - Offre d'emploi - Doctorant en bioinformatique structurale et évolution des protéines (H/F)

emploi.cnrs.fr

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Reposted by Diego Javier Zea

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Apr 17

AlphaFold is amazing but gives you static structures 🧊

In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃

Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...

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Diego Javier Zea @diegozea.bsky.social · Mar 30

Book/Course

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Reposted by Diego Javier Zea

Frank Noe @franknoe.bsky.social · Mar 29

BioEmu is now easily accessible on Colab. Thank you @martinsteinegger.bsky.social and @jjimenezluna.bsky.social !!

@msftresearch.bsky.social

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Mar 29

Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations.
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...

Google Colab

colab.research.google.com

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Diego Javier Zea @diegozea.bsky.social · Mar 6

I have the same question. I haven't checked yet.

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Diego Javier Zea @diegozea.bsky.social · Mar 6

Yes, before, it was pretty cumbersome and slow. Now, it is the opposite experience 🙂

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Diego Javier Zea @diegozea.bsky.social · Mar 6

@googlecolab.bsky.social now has native support for #JuliaLang! 🎉 No special setup is needed anymore—start coding and sharing your @julialang.org projects! 🚀

Screen capture of Google Colab showing their native version of Julia (1.10.8)

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Diego Javier Zea @diegozea.bsky.social · Dec 7

Since you knew it, could it have helped more unconsciously, being there feeding the intuitions? 🤔

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Diego Javier Zea @diegozea.bsky.social · Dec 6

I am not sure that the Julia's Fibonacci implementation is optimal. Using Val is nice to showcase dispatch, but it hits compilation for every number, and it makes the code type unstable. Conversely, using Val should make the compiler memoize the result for each number. github.com/bddicken/lan...

languages/fibonacci/julia/code.jl at bf71f98f0a823775c16fdb79f2445438f471edf6 · bddicken/languages

Compare languages. Contribute to bddicken/languages development by creating an account on GitHub.

github.com

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Reposted by Diego Javier Zea

Jessica Andreani @jessicaandreani.bsky.social · Dec 3

🚨 I am super happy to announce that our analysis of how the structure of protein-RNA interfaces evolves is now published (early access) at @plos.bsky.social Computational Biology:
doi.org/10.1371/jour...
🧬🧶

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Reposted by Diego Javier Zea

Diego del Alamo @delalamo.xyz · Nov 27

Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...

Chai-1 is released under an Apache 2.0 License, which means it can be used for both academic and commerical purposes, including for drug discovery.

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Diego Javier Zea @diegozea.bsky.social · Nov 23

Could you add me to the pack if structural bioinformatics and molecular evolution are welcome?

Diego Javier Zea @diegozea.bsky.social · Nov 22

Thanks :)

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Diego Javier Zea @diegozea.bsky.social · Nov 21

Hi! I nominate myself :)

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Reposted by Diego Javier Zea

Jacob S. Zelko @thecedarprince.bsky.social · Nov 8

Hey folks! I got a bit swamped with all the new #julialang BlueSky people and made my own mega Julia #programmer starter pack!

go.bsky.app/Hv4RKzM

What other starter packs would you want to see? I'm in health research, mathematics, and open source/science. 🧪🛟🩺 📊

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Reposted by Diego Javier Zea

M A Osborne @maosbot.bsky.social · Nov 9

New here? Interested in AI/ML? Check out these great starter packs!

AI: go.bsky.app/SipA7it
RL: go.bsky.app/3WPHcHg
Women in AI: go.bsky.app/LaGDpqg
NLP: go.bsky.app/SngwGeS
AI and news: go.bsky.app/5sFqVNS

You can also search all starter packs here: blueskydirectory.com/starter-pack...

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Reposted by Diego Javier Zea

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Nov 17

This is the first fully open source release of a AF3 like model. Awesome! Congratulations to the team.

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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Diego Javier Zea @diegozea.bsky.social · Nov 19

Hi! I would love to be added to the pack :) Thanks!

Diego Javier Zea @diegozea.bsky.social · Nov 18

Thank you :)

Diego Javier Zea @diegozea.bsky.social · Nov 18

Thanks! :)

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