AlphaFold Unofficial

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!

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.

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/...

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

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.

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

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

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.

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).

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...

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

yep

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

As AI advances, doomers warn the superintelligence apocalypse is nigh AI is advancing fast, and AI doomers say humanity is at risk.

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

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

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

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...

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...

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.

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

Tylenol fights back. Tylenol.com

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

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…

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

🤐 New America 🫡 🇺🇸

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?

AI is an Apex Predator

AlphaFold model of the complex formed between HK2 and the SOX10 5′UTR (189–204 nts). The predicted RNA structure is shown in cyan, and HK2 protein is shown in green. HK2 residues and SOX10 mRNA nucleotides at the interaction interface are highlighted in red. Inset: schematic representation of the secondary structure of the SOX10 5′UTR (189–204 nts) predicted by Mfold, with the putative HK2-binding region (194–198 nts) marked in red.

‬‬Hexokinase 2 (HK2) is known for its metabolic role in #glycolysis. This study shows that it also functions as an #RNAbindingProtein that regulates mRNA translation, particularly of SOX10, promoting #melanoma cell proliferation independently of glycolysis @plosbiology.org 🧪 plos.io/3ViI1qL

There ARE ai's out there really moving humanity forward (google Alphafold for example). Protein folding is the Rosetta Stone of DNA. and it has basically solved it in a couple of years what would have taken humans decades if not centuries.

Not all AI is trash built on theft.

To our surprise, the Piwi* logic isn’t restricted to nuclear Piwi. Immunofluorescence, IP-MS and AlphaFold predictions confirmed that cytoplasmic PIWI proteins also form PIWI* assemblies.
But in this case, the RNA helicase Spindle-E/TDRD9 is being recruited instead of the heterochromatin machinery.

Disney learned nothing from Andor.

No elected official is above our constitutional rights.

The Constitution brought America’s states together into a unified whole that derives its power from the people.

We must call out any action that undermines the principles our founders fought for and protect our democracy.

This is exactly why California is putting out our own, science-backed vaccine recommendations through the West Coast Health Alliance.

We're not going to let the Trump Administration's recklessness put our residents in harm's way.

California is rejecting RFK Jr.'s baseless vaccine restrictions and issuing our own recommendations as part of the West Coast Health Alliance — rooted in evidence, safety, and shared by doctors across the nation.

We won't let the Trump Administration jeopardize our health.

Comedy. Criticism. Commentary. All protected speech. Pulling Jimmy Kimmel off the air is an outrageous act of censorship.

Lower the flags 🇺🇸 half-staff

Farewell Robert Redford

DeepMind’s Demis Hassabis says calling AI PhD Intelligences is ‘Nonsense’ Demis Hassabis, CEO of Google DeepMind, dismissed claims that today’s AI systems are PhD intelligences, calling the label nonsense and arguing that current models lack the consistency and reasoning ne...

Yes but this is coming from the same guy who said AI would heal all diseases in ten years. Is it the season now for liars calling out the liars? Hey Demis, we don’t trust you either.

analyticsindiamag.com/ai-news-upda...