AI research lab DeepMind has created the most comprehensive map of human proteins to date using artificial intelligence. The company, a subsidiary of Google-parent Alphabet, is releasing the data for free, with some scientists comparing the potential impact of the work to that of the Human Genome Project, an international effort to map every human gene.

Proteins are long, complex molecules that perform numerous tasks in the body, from building tissue to fighting disease. Their purpose is dictated by their structure, which folds like origami into complex and irregular shapes. Understanding how a protein folds helps explain its function, which in turn helps scientists with a range of tasks — from pursuing fundamental research on how the body works, to designing new medicines and treatments.

Previously, determining the structure of a protein relied on expensive and time-consuming experiments. But last year DeepMind showed it can produce accurate predictions of a protein’s structure using AI software called AlphaFold. Now, the company is releasing hundreds of thousands of predictions made by the program to the public.

“I see this as the culmination of the entire 10-year-plus lifetime of DeepMind,” company CEO and co-founder Demis Hassabis told The Verge. “From the beginning, this is what we set out to do: to make breakthroughs in AI, test that on games like Go and Atari, [and] apply that to real-world problems, to see if we can accelerate scientific breakthroughs and use those to benefit humanity.”

There are currently around 180,000 protein structures available in the public domain, each produced by experimental methods and accessible through the Protein Data Bank. DeepMind is releasing predictions for the structure of some 350,000 proteins across 20 different organisms, including animals like mice and fruit flies, and bacteria like E. coli. (There is some overlap between DeepMind’s data and pre-existing protein structures, but exactly how much is difficult to quantify because of the nature of the models.) Most significantly, the release includes predictions for 98 percent of all human proteins, around 20,000 different structures, which are collectively known as the human proteome. It isn’t the first public dataset of human proteins, but it is the most comprehensive and accurate.

If they want, scientists can download the entire human proteome for themselves, says AlphaFold’s technical lead John Jumper. “There is a HumanProteome.zip effectively, I think it’s about 50 gigabytes in size,” Jumper tells The Verge. “You can put it on a flash drive if you want, though it wouldn’t do you much good without a computer for analysis!”

After launching this first tranche of data, DeepMind plans to keep adding to the store of proteins, which will be maintained by Europe’s flagship life sciences lab, the European Molecular Biology Laboratory (EMBL). By the end of the year, DeepMind hopes to release predictions for 100 million protein structures, a dataset that will be “transformative for our understanding of how life works,” according to Edith Heard, director general of the EMBL.

The data will be free in perpetuity for both scientific and commercial researchers, says Hassabis. “Anyone can use it for anything,” the DeepMind CEO noted at a press briefing. “They just need to credit the people involved in the citation.”

THE BENEFITS OF PROTEIN FOLDING

Understanding a protein’s structure is useful for scientists across a range of fields. The information can help design new medicines, synthesize novel enzymes that break down waste materials, and create crops that are resistant to viruses or extreme weather. Already, DeepMind’s protein predictions are being used for medical research, including studying the workings of SARS-CoV-2, the virus that causes COVID-19.

New data will speed these efforts, but scientists note it will still take a lot of time to turn this information into real-world results. “I don’t think it’s going to be something that changes the way patients are treated within the year, but it will definitely have a huge impact for the scientific community,” Marcelo C. Sousa, a professor at the University of Colorado’s biochemistry department, told The Verge.

Scientists will have to get used to having such information at their fingertips, says DeepMind senior research scientist Kathryn Tunyasuvunakool. “As a biologist, I can confirm we have no playbook for looking at even 20,000 structures, so this [amount of data] is hugely unexpected,” Tunyasuvunakool told The Verge. “To be analyzing hundreds of thousands of structures — it’s crazy.”

Notably, though, DeepMind’s software produces predictions of protein structures rather than experimentally determined models, which means that in some cases further work will be needed to verify the structure. DeepMind says it spent a lot of time building accuracy metrics into its AlphaFold software, which ranks how confident it is for each prediction.

Predictions of protein structures are still hugely useful, though. Determining a protein’s structure through experimental methods is expensive, time-consuming, and relies on a lot of trial and error. That means even a low-confidence prediction can save scientists years of work by pointing them in the right direction for research.

Helen Walden, a professor of structural biology at the University of Glasgow, tells The Verge that DeepMind’s data will “significantly ease” research bottlenecks, but that “the laborious, resource-draining work of doing the biochemistry and biological evaluation of, for example, drug functions” will remain.

Sousa, who has previously used data from AlphaFold in his work, says for scientists the impact will be felt immediately. “In our collaboration we had with DeepMind, we had a dataset with a protein sample we’d had for 10 years, and we’d never got to the point of developing a model that fit,” he says. “DeepMind agreed to provide us with a structure, and they were able to solve the problem in 15 minutes after we’d been sitting on it for 10 years.”

WHY PROTEIN FOLDING IS SO DIFFICULT

Proteins are constructed from chains of amino acids, which come in 20 different varieties in the human body. As any individual protein can be comprised of hundreds of individual amino acids, each of which can fold and twist in different directions, it means a molecule’s final structure has an incredibly large number of possible configurations. One estimate is that the typical protein can be folded in 10^300 ways — that’s a 1 followed by 300 zeroes.

Because proteins are too small to examine with microscopes, scientists have had to indirectly determine their structure using expensive and complicated methods like nuclear magnetic resonance and X-ray crystallography. The idea of determining the structure of a protein simply by reading a list of its constituent amino acids has been long theorized but difficult to achieve, leading many to describe it as a “grand challenge” of biology.

In recent years, though, computational methods — particularly those using artificial intelligence — have suggested such analysis is possible. With these techniques, AI systems are trained on datasets of known protein structures and use this information to create their own predictions.