11/12 All the course information, the link to the slides, and more can be found on my site in GithubPages. In addition, YouTube has automatically dubbed the course into 18 other languages to make learning more accessible.
I hope you find it useful :)
miangoaren.github.io/teaching/pro...
11/12 I also created this GitHub repository with:
+300 tools organized into 25 categories
+70 databases (12 categories)
+130 learning resources (9 categories)
github.com/miangoar/AI-...
Among them, I want to highlight this other free course by
Kieran Didi
structural-bioinformatics.netlify.app
10/12 In the final lecture "Data & biases" (4h 16min), we discuss the main biological databases (eg. PDB, UniProt, NCBI), data cleaning strategies, data leakage, and the biases that can silently affect the generalization capabilities of your models
youtu.be/bEt7tZKvfiI
9/12 In the 9th lecture "AI-driven protein design" (8h 27min), we cover the design toolkit: from directed evolution and rational design, to protein language models (representation learning) and generative AI to create both protein sequences and structures
youtu.be/PvMNlxZv_Bg
8/12 In the 8th lecture "AlphaFold" (7h 39mins), we review in detail the AF2 and AF3 architectures, how they revolutionized structural biology, their strengths and weaknesses and what the post-AlphaFold era looks like for protein design
youtu.be/4K8SDxk85a0
7/12 In the 7th lecture "Protein evolution" (2h 38mins, and my personal favorite), we trace how proteins originated from simple peptides, how mutations shape the evolutionary paths and how epistasis drives the evolution of proteins
youtu.be/rkmWSR8BUms
6/12 In the 6th lecture "Protein function" (1h 58mins), we cover how proteins fold inside the cell, how enzymes work and how function is regulated through distinct mechanisms like allostery, post-translational modifications, and proteostasis
youtu.be/Un6QaTM412A
5/12 In the 5th lecture "Protein structure" (2h 55mins), we explore the principles of structural biology: from amino acids and secondary structure to fold classification schemes and the uneven shape of the protein universe
youtu.be/7GmPNVhJhw0
4/12 In the 4th lecture "Transformers & language models" (3h 42mins), we break down how the original Transformers architecture work, the differences between BERT and GPT, scaling laws, modern LLMs and how to work with them
youtu.be/tNAKnz_tDIc
3/12 In the 3rd lecture "Deep learning" (1h 54mins), we’ll review how neural networks work, from neurons and backpropagation to modern architectures. Then we explore the main DL frameworks used to build models
youtu.be/YiEmCQuW-xc
3/12 In the 2nd lecture "Machine learning" (1h 39mins), we’ll review what artificial intelligence is and its subfields, the current capabilities of the algorithms, and how a model is trained in general
youtu.be/9fEl5RsLKJs
2/12 In the first lecture "Basic computing concepts" (1h 58mins), we’ll review how CPUs and GPUs work, as well as essential software for data analysis like GNU/Linux and the python ecosystem for bioinformatics
youtu.be/RddVvvYRpTc
1/12 🧵 Do you want to learn how to design proteins using AI but don’t know anything about biology?
I created a free 10-lesson course on YouTube. It’s now available in Spanish (original) and English (autodubbing w/Kokoro 82M).
Here’s an overview of the topics covered in each lecture :)
AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions
📄 research.nvidia.com/labs/dbr/ass...
🌐 alphafold.ebi.ac.uk
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...
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.
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
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
