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Albert Vilella, PhD. @albertvilella.bsky.social · 2d

@ewanbirney.bsky.social on the new version of Alphafold at the @emblebi.bsky.social
www.ebi.ac.uk/about/news/t...
AlphaFold has been a transformation not just in structural biology but also - due to its ability to be applied to all proteins - to molecular biology as a whole.

EMBL-EBI and Google DeepMind renew partnership and release update to AlphaFold Database

Deeper collaboration between EMBL-EBI and Google DeepMind brings updates to the AlphaFold Database.

www.ebi.ac.uk

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Reposted by AlphaFold Unofficial

Albert Vilella, PhD. @albertvilella.bsky.social · 2d

A huge part of this broad reach has been the collaboration between European Bioinformatics Institute | EMBL-EBI and Google DeepMind on AlphaFoldDB - AlphaFold database - running AlphaFold as baseline for all known proteins,

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Journal of Experimental Botany @jxbotany.bsky.social · 1d

📝 SPECIAL ISSUE REVIEW 📝

Hoernstein et al. consolidate information on Acylamino acid-releasing enzyme, a serine protease affecting plant development & aging, & emphasize its conserved features across all kingdoms of life 🌱🦠🧫

🔗 doi.org/10.1093/jxb/...

#PlantScience 🧪 @reskilab.bsky.social

Fig. 3 (shortened, full legend in paper): Summary of the current knowledge of acylamino acid-releasing enzyme (AARE) localization and function in plants and animals. AtAARE (green) is depicted as plant AARE and human AARE (blue) as animal AARE. Structures of both isoforms (AF-Q84LM4-F1, AF-P13798-F1; https://alphafold.ebi.ac.uk/) were predicted with AlphaFold (Jumper et al., 2021; Varadi et al., 2024). Middle shows commonalities between plants and animals: Localization of AARE to the nucleus and to the cytosol has been shown in Arabidopsis and human cell lines (Shimizu et al., 2003; Nakai et al., 2012; Zeng et al., 2017; Hoernstein et al., 2023). AARE functions as part of the antioxidant defence system in plants and animals (Shimizu et al., 2003; Nakai et al., 2012; Gogliettino et al., 2014; Riccio et al., 2015; Zeng et al., 2017). Left (only plants): AARE localizes to both plastids and mitochondria in plants (Hoernstein et al., 2023).

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Reposted by AlphaFold Unofficial

Maxim Tsenkov @mitsenkov.bsky.social · 3d

The latest #AlphaFold DB update is out!

We synchronised with UniProt release 2025_03, predicted protein isoforms across all species, and provide MSAs used to generate each prediction.

Proud of the team at the PDBe for the hard work that went into this. Grateful to play my part in it!

EMBL-EBI @ebi.embl.org · 3d

We’re renewing our collaboration with Google DeepMind!

We'll keep developing the AlphaFold Database to support protein science worldwide 🎉

To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.

www.ebi.ac.uk/about/news/t...

🖥️🧬 #AlphaFold
@pdbeurope.bsky.social

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Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · 3d

You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.

This saves some clicking around. Neat!

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EMBL-EBI @ebi.embl.org · 3d

We’re renewing our collaboration with Google DeepMind!

We'll keep developing the AlphaFold Database to support protein science worldwide 🎉

To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.

www.ebi.ac.uk/about/news/t...

🖥️🧬 #AlphaFold
@pdbeurope.bsky.social

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Reposted by AlphaFold Unofficial

Julia M. Rohrer @dingdingpeng.the100.ci · 9d

Cool episode on how AI can help us design new proteins (e.g., for vaccines).

I’d heard of AlphaFold before, but not of ProteinMPNN. You feed a protein structure into PMPNN & generate possible sequences of amino acids. And then you feed those into AlphaFold to check whether they’d fold up that way!

Saloni @scientificdiscovery.dev · 9d

New episode of HARD DRUGS!

AlphaFold, ProteinMPNN & other AI tools are transforming biology and drug design.

But how do they work? What can’t they do? And can we use them to make a vaccine against Strep A for the very first time?

In this episode, Jacob and I talk about hacking proteins with AI.

Hacking proteins with AI

open.spotify.com

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Reposted by AlphaFold Unofficial

Roni Odai @rodai.bsky.social · 9d

Viral AlphaFold Database (VAD) is live in Science Advances

~27,000 predicted viral protein monomers & homodimers

Conserved folds across bacteria, archaea & eukaryotic viruses

New toxin–antitoxin system KreTA uncovered

Vast “functional darkness” remains uncharted

www.science.org/doi/10.1126/...

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.

www.science.org

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 8d

Visiting Ephesus at #embointegmod25 to look for the missing AlphaFold 3 code

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Cameron Thrash @jcamthrash.bsky.social · 8d

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes www.science.org/doi/full/10.... #jcampubs

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.

www.science.org

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Daniel Asarnow @dabiophysicist.bsky.social · 8d

Is it normal for SimpleFold to leave a bunch of stuff tangled in a knot right on top of the packed core of the rest of the structure (clashing terribly)? Alpha would loop it around the outside, maybe feed the active site its own tail...definitely less jarring #alphafold

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Maite Colinas @maitecolinas.bsky.social · 8d

How does it catalyze iridoid cyclization? Well, we don’t know its catalytic mechanism in detail yet, that will be the subject of future research. We do know it retains general esterase activity but based on mutagenesis studies this esterase activity is not essential for cyclization (unsurprising).

A phylogenetic tree showing ICYC is related to methylesterases next to sequencing logos of selected amino acid residues of the active site. The esterase catalytic triad of serine, aspartate and histidine is completely conserved. Next to it an alphafold predicted structure of the ICYC active site with assumed substrate 8-oxocitronellyl enol docked.

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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 11d

"AlphaFold-Multimer’s prediction accuracy is sensitive to the defined boundaries of the interacting partners" #alphafold

yep

www.pnas.org/doi/10.1073/...

AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions | PNAS

Interactions mediated by intrinsically disordered protein regions (IDRs) pose formidable challenges in structural characterization. IDRs are highly...

www.pnas.org

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NPR @npr.org · 16d

AI is advancing fast, and AI doomers say humanity is at risk.

As AI advances, doomers warn the superintelligence apocalypse is nigh

AI is advancing fast, and AI doomers say humanity is at risk.

n.pr

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Mann Lab @mannlab.bsky.social · 16d

2/
AI has had major breakthroughs (#alphafold #chatgpt) & computational models can now detect patterns in complex datasets without external guidance 🧠🖥️

🧬 biological datasets often contain entangled information making them complex to interpret →🧠🖥️ + 🧬 = unlock new biology

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Francesca Bellazzi @frabellazzi.bsky.social · 16d

I was in Rome for the Emergence in Philosophy&Science summer school and workshop. I gave an overview lecture on emergence in biochemical contexts and a new talk on #AlphaFold and the implications of using AI in science for reductionism.
Thanks to the organisers!
#FunMo @leverhulme.ac.uk

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Simon Dürr @simonduerr.eu · 15d

We are hiring a PhD student 🎓

Work with me and Matthias Rüdt in our department on an exciting industry collaboration with Lonza combining high-throughput experiments and molecular modelling using AlphaFold and MolecularDynamics

📍 Sion, Valais, Switzerland

More info: www.jobup.ch/fr/emplois/d...

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Das Lab @rdaslab.bsky.social · 16d

The results are in: top codes in Stanford #RNA 3D Folding @kaggle.com competition are competitive with CASP16-leading humans Vfold, beat AlphaFold 3. Top team’s trick was template-based modeling, not #DeepLearning. Congrats: john, odat, Eigen, + all 1706 participants! www.kaggle.com/competitions...

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Alana Kinrich @alanakinrich.medsky.social · 18d

I took Tylenol as needed throughout my pregnancy. I am a doctor. I order Tylenol for pregnant women regularly. Tylenol is safe in pregnancy. RFK Jr is ignoring a huge recent well-done study because he doesn't like the answer it gives. There is no causality between Tylenol and autism.

Caroline Dodds Pennock @carolinepennock.bsky.social · 18d

You have no idea how much I despite these anti-science dipshits for making pregnant women terrified of taking (safe, mild, proven) pain relief.

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Stonekettle @stonekettle.bsky.social · 18d

So, they're going to blame women and Tylenol.

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Cath RN, PhD 🎃 @headdoc35.bsky.social · 17d

Tylenol fights back. Tylenol.com

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Saganism @sagan.bsky.social · 19d

We live in a society exquisitely dependent on science and technology, in which hardly anyone knows anything about science and technology.

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Tominaga K. (tomiken) @pacyc184.bsky.social · 20d

Cyanobacteriochrome-like GAF folds in phages revealed via AlphaFold proteomic modelling - ScienceDirect https://www.sciencedirect.com/science/article/pii/S2001037025003800

Cyanobacteriochrome-like GAF folds in phages revealed via AlphaFold proteomic modelling

Accurate protein structure prediction followed by structural homology detection enable the functional annotation of otherwise obscure viral protein-co…

www.sciencedirect.com

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AlphaFold Unofficial @alphafold.bsky.social · 19d

🤐 New America 🫡 🇺🇸

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AlphaFold Unofficial @alphafold.bsky.social · 19d

Since the Government is buying TikTok and will control the Algorithm.
The U.S. Government will do to TikTok what Elon has done to Twitter.

BlueSky, what alternative platforms do you support?

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