Google's DeepMind Predicts 3D Shapes of Proteins

Google's DeepMind is using an AI program, called AlphaFold, to predict the 3D shapes of proteins, the fundamental molecules of life. 'DeepMind set its sights on protein folding after its AlphaGo program famously beat Lee Sedol, a champion Go player, in 2016,' reports The Guardian. The company says 'It's never been about cracking Go or Atari, it's about developing algorithms for problems exactly like protein folding.' From the report: DeepMind entered AlphaFold into the Critical Assessment of Structure Prediction (CASP) competition, a biannual protein-folding olympics that attracts research groups from around the world. The aim of the competition is to predict the structures of proteins from lists of their amino acids which are sent to teams every few days over several months. The structures of these proteins have recently been cracked by laborious and costly traditional methods, but not made public. The team that submits the most accurate predictions wins. On its first foray into the competition, AlphaFold topped a table of 98 entrants, predicting the most accurate structure for 25 out of 43 proteins, compared with three out of 43 for the second placed team in the same category.

To build AlphaFold, DeepMind trained a neural network on thousands of known proteins until it could predict 3D structures from amino acids alone. Given a new protein to work on, AlphaFold uses the neural network to predict the distances between pairs of amino acids, and the angles between the chemical bonds that connect them. In a second step, AlphaFold tweaks the draft structure to find the most energy-efficient arrangement. The program took a fortnight to predict its first protein structures, but now rattles them out in a couple of hours.

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