Protein-folding AI heralds new era in digital biology

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By Rich Pell

DeepMind, the artificial intelligence subsidiary of Alphabet, has announced that its AlphaFold AI system used to predict the 3D structure of a protein has now predicted structures for nearly all catalogued proteins known to science. This will expand the AlphaFold Protein Structure Database by over 200x – from nearly 1 million structures to over 200 million structures – with the potential to dramatically increase our understanding of biology, say the researchers.

This update includes predicted structures for plants, bacteria, animals, and other organisms, opening up many new opportunities for researchers to use AlphaFold to advance their work on important issues, including sustainability, food insecurity, and neglected diseases. The update, say the researchers, means that most pages on the main protein database UniProt will come with a predicted structure, and all 200+ million structures will also be available for bulk download via Google Cloud Public Datasets, making AlphaFold even more accessible to scientists around the world.

“AlphaFold is the singular and momentous advance in life science that demonstrates the power of AI,” says Eric Topol, Founder and Director of the Scripps Research Translational Institute. “Determining the 3D structure of a protein used to take many months or years, it now takes seconds. AlphaFold has already accelerated and enabled massive discoveries, including cracking the structure of the nuclear pore complex. And with this new addition of structures illuminating nearly the entire protein universe, we can expect more biological mysteries to be solved each day.”

The nuclear pore complex is considered one of the most fiendish puzzles in biology. The giant structure consists of hundreds of protein parts and controls everything that goes in and comes out of the cell nucleus. Its delicate structure was finally revealed by using existing experimental methods to reveal its outline and AlphaFold predictions to complete and interpret any areas that were unclear.

AlphaFold is already having a significant, direct impact on human health, say the researchers. Meeting with researchers at the European Society of Human Genetics revealed how important AlphaFold structures are to biologists and clinicians trying to unravel the causes of rare genetic diseases. In addition, AlphaFold is accelerating drug discovery by providing a better understanding of newly identified proteins that could be drug targets, and helping scientists to more quickly find potential medicines that bind to them.

“AlphaFold has launched biology into an era of structural abundance, unlocking scientific exploration at digital speed,” says Demis Hassabis, CEO of DeepMind Technologies. “The AlphaFold DB serves as a ‘google search’ for protein structures, providing researchers with instant access to predicted models of the proteins they’re studying, enabling them to focus their effort and expedite experimental work. From fighting disease to developing vaccines, AlphaFold has already enabled incredible advances on some of our biggest global challenges, and this is just the beginning of the impact that we will start to see over the next few years. Our hope is that this expanded database will aid countless more scientists in their work and open up completely new avenues of scientific exploration, such as metaproteomics.”

“At DeepMind, we’re hard at work building on all this potential with significant investments in many areas, including partnering with our new sister Alphabet company Isomorphic Labs to reimagine the entire drug discovery process from first principles with an AI-first approach; establishing a wet lab at the renowned Francis Crick Institute to strengthen the connection between AI and experimental techniques to advance understanding of biology, including protein design and genomics; and expanding our AI for Science team to accelerate further progress on our fundamental biology research and apply AI to other fascinating and important scientific challenges, such as climate science, quantum chemistry, and fusion.”

As pioneers in the emerging field of ‘digital biology,’ say the researchers, they are excited to see the huge potential of AI starting to be realized as one of humanity’s most useful tools for advancing scientific discovery and understanding the fundamental mechanisms of life.



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