Alphabet’s DeepMind AI has solved “the protein folding problem” that could aid medicine research

TL;DR: DeepMind Technologies, a research lab in the UK owned by Alphabet, has developed an AI that can determine the folded shape of a protein in a matter of hours, which would typically require months or years of lab research. Depending on how Alphabet distributes this technology to the science community, this development has the potential to affect a huge array of medical and biological research.

Computer scientists at DeepMind, a lab owned by Alphabet, Google’s parent company, have developed an AI that has made a monumental leap in solving “the protein folding problem.” This conundrum has plagued biologists for decades, and solving it can accelerate countless other studies in medicine, agriculture, and conservation, to name a few.

Proteins are crucial “macromolecules” built from strings of molecules called amino acids. These strings of molecules are built inside of each cell by reading an organism’s DNA and blocking together long chains of amino acids. Of the 20 amino acids that make up proteins, each one chosen depends on the DNA sequence being read, and each amino acid has special properties that cause the long chain of molecules to fold over itself into a very specific, highly complicated shape, which gives the protein its function.

Understanding the shape and how it relates to the function of proteins is so important because they are responsible for most biological functions in the body, including immune response, digestion, energy production, muscle contraction, blood clotting, and countless more.

The interest of many research groups revolves around synthetic proteins used in medicines. Knowing the order of amino acids in a protein is easy enough for researchers if they know the DNA sequence that is used as its template, but knowing its shape can dramatically expedite the process of determining how it will function in people, bacteria or viruses. Among other mysteries this can unravel, think of vaccine research, a topic on everyone’s mind presently.

DeepMind’s neural network can quickly and reliably determine a protein’s shape, given the string of amino acids that comprise the protein.

Scientists have been working hard to crack this nut for over 50 years. A competition called the Critical Assessment of Structure Prediction (CASP) was formed 25 years ago to bring together this research, compare results and spur on investigation.

No one has really come close to solving this problem until DeepMind came onto the scene. Tested on a variety of proteins, DeepMind’s neural network was able to accurately assume the folded structure of a protein with the precision of lab-based experiments that typically take months or years to solve.

It should be noted that experts say solving the protein folding problem speeds up just the initial stage of the long process of safely developing a medication.

This has also apparently emerged too late to affect vaccine research into the coronavirus but could be used down the line to stem future pandemics, determine whether existing medications can be used on novel infections, and research genetic diseases such as Alzheimer’s.

John Moult, a University

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A Malaria Mystery, Partly Solved: What Happens When the Rains End?

But during the dry season, the researchers found, the parasites in most red blood cells stopped making the sticky versions of that protein. They slipped away into the spleen to their destruction. But a few clingy survivors hung on, and appeared to slow down their metabolism, like microscopic bears hibernating for the winter.

This had two effects that protected them.

First, by measuring the inflammatory proteins produced by the immune system, Dr. Portugal showed that the reclusive parasites had somehow become too “quiet” to trigger the immune counterattack that might destroy them.

Second, too few sticky cells remained to clog brain capillaries, so even infected children survived.

“A parasite that kills its host during the dry season reaches a dead end,” Dr. Portugal said.

Sarah K. Volkman, a molecular biologist at Harvard’s T.H. Chan School of Public Health and a leading malaria expert, called the new study “important.” Dr. Volkman’s research in Senegal has found that parasite lineages persisted in villages for 10 years. She noted that understanding the importance of that small dry-season reservoir could reveal ways to destroy the parasites when they are at their weakest.

Dr. Miriam K. Laufer, a malaria specialist at the University of Maryland’s medical school, also praised the study, saying it “delivered concrete data about things we thought were the case, such as that the dry season infections do not elicit a big immune response.”

Dr. Nicholas J. White, director of a malaria research unit based at the University of Oxford and Mahidol University in Thailand, was more reserved, noting that researchers in Vietnam had previously shown that parasites persist in dry months.

Parasites might simply “change their clothes” every few cycles to avoid being recognized by the immune system, he argued, and the lower number of cells clinging to walls could be explained by a change in the host’s antibody response rather than by a change in the parasite.

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