AlphaFold Cracks Protein Folding - Scientific Breakthrough by DeepMind

Exciting news comes out of DeepMind, the Google-owned research group that developed AlphaGo the first computer program to defeat a Go world champion. This time, the DeepMind team has developed AlphaFold, an artificial intelligence based system that cracked protein folding. In this video, we’ll explain what protein folding is, and why AlphaFold is an exciting news for the scientific community, but also for the tech community.

0:00 Intro
0:24 Proteins Explained
1:18 Amino Acids
1:41 Protein Folding Problem
2:13 AlphaFold
2:40 CASP
3:15 AlphaFold's Achievement
4:45 Impact on Scientific World
5:23 Thank You

Proteins are tiny molecular machines. Inside every cell of your body there are billions of proteins hard at work. They allow your eyes to detect light, your neurons to fire and much much more. But proteins are not only found in humans. They are present in all living things. Proteins are fundamental to all of life.

If we could understand how proteins actually look, their 3 dimensional shapes, we could develop better drugs, and do it faster and cheaper. It could even unlock new possibilities such as breaking down plastic waste or efficiently capturing carbon from the atmosphere using proteins and enzymes.

But in the past 50 years science has made slow progress at understanding proteins. We’ve figured out the structure of only 0.1% of the known proteins.

Why has progress been so slow? Well..., because proteins are really complex. In principle, they are a simple chain of these building blocks called amino acids. The problem is that these amino acids interact with each other. Some amino acid pairs attract each other, others push themselves apart. A protein has hundreds of amino acids, all pushing and pulling in all directions, making the protein fold in hard to predict ways. Each protein is a self organising origami with 10^300 possible conformations, but only a few stable shapes. Finding these stable shapes is called the “Protein Folding” problem and it has baffled scientists all around the world for decades. The existing experimental techniques that scientists have used so far are slow and expensive. It takes years to figure out the stable shape of a protein.

The DeepMind team behind AlphaFold has taken a completely different approach than the traditional one. They loaded the 170,000 known protein structures into an AI model and have simulated the interactions between the amino acids. Their model predicts the stable shape of any protein. Since it’s all digital, not based on physical experiments, it’s much faster and cheaper. But is it better? How do you know that the prediction is accurate?

In 1994 a group of scientists started CASP, which is basically the Olympics of Protein Folding. Every 2 years, the organisers publish a list of proteins with unknown structures. Teams all around the world submit their predictions. Then the true structure of those proteins is revealed and a score between 0 and 100 is given to each prediction. A score of 90 or better means that your prediction is on par with experimental results. Before DeepMind published their results, the top scores were only 40. The first version of AlphaFold achieved a score of 60. And now, the second version achieved an astonishing score of 92.

It’s difficult to grasp the impact of this achievement. There are over 200 million proteins with unknown folding structures. This whole mystery could go away if DeepMind finds a way to make their technology available. Scientists and enthusiasts around the world would then be free to work on better medicines and health treatments, technology to tackle the climate crisis and pollution.

And equally important is the example we are setting to the younger generation. We’re showing them that science, technology and machine learning are used to improve lives. Technology is not just bits on a screen, it delivers tangible improvements to all of us.

Resources:
* The Inner Life of the Cell, BioVision at Harvard University - https://xvivo.com/inner-life-of-the-cell/
* AlphaFold: The making of a scientific breakthrough - https://www.youtube.com/watch?v=gg7WjuFs8F4
* Protein folding explained
, DeepMind - https://www.youtube.com/watch?v=KpedmJdrTpY
* AlphaFold: a solution to a 50-year-old grand challenge in biology, DeepMind - https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology

Thumbnail Credit:
https://commons.wikimedia.org/wiki/File:Alpha_helix.png
en:User:Bikadi, CC BY-SA 3.0 http://creativecommons.org/licenses/by-sa/3.0 via Wikimedia Commons

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