Biomedical Treasure Chest

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DeepMind opened access to AlphaFold, a model that finds the shapes of proteins, and to its output so far — a potential cornucopia for biomedical research.
What’s new: The research lab, a division of Google’s parent company Alphabet, made AlphaFold freely available. It also opened databases that contain hundreds of thousands of three-dimensional protein shapes.
Shapes of things to come: Proteins are molecules made up of chains of amino acids. They perform myriad biological functions depending on the way the chain folds, and understanding their shapes can shed light on what they do and how they do it. Protein shapes are determined by the proximity of essential portions, or residues, of amino acids. AlphaFold finds likely shapes by optimizing possible structures that keep residues close to one another based on their positions and angles. For a description of how it works, see “Protein Shapes Revealed” here.

  • The company published research that describes how to use AlphaFold to find the shapes of both general and human-specific proteins.
  • The model has analyzed the structure of roughly 98 percent of proteins found in the human body. It has analyzed hundreds of thousands more in 20 other organisms commonly used by researchers such as e.coli, fruit flies, and soybeans.
  • The company plans to release an additional 100 million protein structures by the end of 2021. Such data is published and maintained by the European Molecular Biology Laboratory.

Behind the news: Until recently, scientists had to rely on time-consuming and expensive experiments to figure out protein shapes. Those methods have yielded about 180,000 protein structures. AlphaFold debuted in 2018, when it won an annual contest for predicting protein structures. A revised version of the model won again in 2020 with an average error comparable to the width of an atom.
Why it matters: Biologists could use these tools to better understand the function of proteins within the human body and develop new treatments for some of medicine’s most vexing maladies. Researchers already are using AlphaFold data to devise treatments for maladies including Covid-19 and several common, deadly tropical diseases.
We’re thinking: We applaud DeepMind’s decision to make both its landmark model and the model’s output available for further research. We urge other companies to do the same.

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