GAMA Miguel Angel

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n
doi.org/10.64898/202...

a close up of a person holding a gun in a dark room ALT: a close up of a person holding a gun in a dark room

Me watching how I'm not part of the cool guy's cluster :(

I am in the "Life Sciences Super Cluster" and quite far away from many colleagues in protein design who are in the cluster called "Computational Chemistry Nexus" 😭

Does anyone know the meaning of AlphaGenome and its impact? It’s not my area, so I don’t know how important it is. But I think is not equivalent to AlphaFold2, since no other area in biology has the high-quality data and structure provided by PDB, UniProt and CASP competition.

Sometimes I see Nature papers as elegant $13k commercials from AI companies inviting you to subscribe to their chatbots

How does catalysis emerge from non-catalytic domains?

In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.

A striking case of catalysis evolving from binding.

Ancient amino acid sets enable stable protein folds Early proteins likely arose from a chemically limited set of amino acids available through prebiotic chemistry, raising a central question in molecular evolution: could such primitive compositions yie...

Can proteins fold and function with half of the amino acid alphabet?
Using only 10 residues, we designed stable, mutation-resilient structures—no aromatics or basics involved.
A minimalist foundation for ancient biology and synthetic design. tinyurl.com/37t8br4v
#ProteinDesign #OriginsOfLife

I recorded ~4h where we cover the main bio databases, data processing methods, many sources of bias and topics like generalization and data leakage :)
youtu.be/SKpHaHgvCKE

Slides
drive.google.com/file/d/1jpEwDBncJCRviG_DaWs2EpzCL_1BfB9t/view

English is available only via auto-translated subtitles

I recorded ~8h introducing the main algorithms for protein design: from classical approaches to protein language models, AlphaFold, ESMFold, MPNN, diffusion models and more :)
youtu.be/wKUYtAt87d4T...

Slides
drive.google.com/file/d/1EPLj...

English is available only via auto-translated subtitles

I’ve recorded ~8h explaining the architectures of AlphaFold, AF2 & AF3, as well as the context needed to understand their development, applications and limitations :)
youtu.be/_jDRr5BcTaY

Slides
drive.google.com/file/d/1i4QE...

English is available only via auto-translated subtitles

2/2 I’ve reviewed many courses, yet few give evolution the importance it deserves. They acknowledge it, but rarely go beyond algorithms like AlphaFold. Understanding evolution helps us understand how our models are biased and how to mitigate those biases.

The 7th lecture is available on YouTube :) We will review how proteins emerge and diversify throughout evolution, considering mutations and molecular interactions
youtu.be/qaypRS8SX5M

Slides
drive.google.com/file/d/1BfQd...

English is available only via auto-translated subtitles

Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years - Nature Communications The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient microbes shaped Earth’s nitrogen cycle and offering a new experimental ...

Our new paper, out today! We resurrected ancient nitrogenases first used by life on Earth 3 billion years ago. We combined synthetic biology and geology & validated their chemical #biosignature in rocks that helps reveal ancient life on Earth!(and beyond!)

Link: www.nature.com/articles/s41...

💪 NEW VIDEO:
Flying over the A-band of an atomic-scale model of a vertebrate muscle sarcomere. Let's explore the molecular mechanics that make your muscles work.

Rendered using @bradyajohnston.bsky.social 's molecular nodes

Model based on the incredible work of the @raunser-lab.bsky.social lab

The 6th lecture is now available on YouTube :) We’ll review how proteins adopt their 3D shape, how they perform their functions and how their activity is regulated
youtu.be/cZs8XtVYa5A

Slides
drive.google.com/file/d/1TpPj...

English is available only via auto-translated subtitles

The fifth lecture of the course is now available on YouTube :) We’ll review amino acid chemistry and how we organize and classify proteins
youtu.be/gE6qXwpBP_s

Slides
drive.google.com/file/d/1F99V...

For now, the English version is only available through the automatic translation of the subtitles

The fourth lecture of the course is now available on YouTube :) We will review how Transformers and modern LLMs work
youtu.be/vUpb6O6T2yQ

Slides
drive.google.com/file/d/1y2Vj...

For now, the English version is only available through the automatic translation of the subtitles.

Thanks!

Where is the preprint? 🧐

The third lecture of the course is now available on YouTube :) We will review how neural networks work.
youtu.be/pAgL7NsCUMU

Slides
drive.google.com/file/d/1cazt...

For now, the English version is only available through the automatic translation of the subtitles.

The second lecture of the course is now available on YouTube :) We will review what AI is, its subfields and how to train a model.
youtu.be/Xx80O85-5rI

Slides
drive.google.com/file/d/1i-Jo...

For now, the English version is only available through the automatic translation of the subtitles.

The first lecture of the course is now available on YouTube :)
youtu.be/uMkZzKbnoJI

Slides
drive.google.com/file/d/1uDwe...

For now, the English version is only available through the automatic translation of the subtitles.

Sorry, i forgot to add the webpage of the course 😅

miangoaren.github.io/teaching/pro...

By the way, if anyone has recommendations on how to translate the classes (e.g., the audio) into English, they’re very welcome. My YouTube account doesn’t have the stats required to use automatic dubbing 😢

GitHub - miangoar/AI-driven-protein-design: Resources for learning AI-driven protein design Resources for learning AI-driven protein design. Contribute to miangoar/AI-driven-protein-design development by creating an account on GitHub.

3/3 I also created a repository with +300 tools, +70 databases and +130 courses related to protein science, bioinformatics and data science, aimed at facilitating learning. Once all classes have been published, the slides will be available for download :)

github.com/miangoar/AI-...

2/3 The course includes +800 freely available slides, and starting next monday, I will publish one video per day. For example, the AlphaFold lecture is ~7.4 hours long and includes 148 slides, in which I cover the architectures of AF1, AF2 and AF3 as well as their applications.

🧵1/3 I created this free 37-hour course, distributed across 10 lectures, to introduce AI-based protein design. For more information about the course and its specific topics, please visit the official course page:

Biomedical and life science articles by female researchers spend longer under review Women are underrepresented in academia, especially in STEMM fields, at top institutions, and in senior positions. This study analyzes millions of biomedical and life science articles, revealing that f...

Cost of being female lead/corresponding author in biomedical sciences: "[T]he median amount of time spent under review is 7.4%–14.6% longer for female-authored articles than for male-authored articles" even in disciplines where women well-represented. #AcademicSky

journals.plos.org/plosbiology/...

😮 OMG! Congratulations Milot !