DeepMind AI has unlocked the 'protein universe' - and it could help cure Parkinson's disease

DeepMind AI has unlocked the ‘protein universe’ – and it could help cure Parkinson’s disease

British scientists have used artificial intelligence (AI) to create a database of the ‘entire protein universe’ that could help pave the way for a cure for Parkinson’s disease, along with other breakthroughs scientists.

DeepMind, a London-based company owned by Alphabet, the Silicon Valley tech giant that owns Google, first revealed its AlphaFold technology last year when it contained the 3D shape and structure of around 350 000 proteins.

Now the database has grown to over 200 million proteins, that’s almost every protein known to science and covers animals, proteins, bacteria and everything in between.

By accurately distinguishing what proteins actually look like from their genetic code, scientists can predict how they will interact with other proteins, antibodies and drugs.

“When we launched it last July, it was recognized as a big step forward for biology,” said Dr. Demis Hassabis, CEO and Founder of DeepMind.

“It was also a great demonstration of how AI can be used to advance scientific discovery and provided structural biologists with this powerful new tool to find the 3D structure of a protein almost as easily as a keyword search on Google and, as we know, the 3D structure of proteins is key to understanding their function.

“You can think of [AlphaFold] as covering the whole universe of proteins.

He added that more than half a million scientists have already used the ever-expanding directory for a myriad of projects.

“A whole universe in one click”

Professor Ewan Birney, Deputy Director General of the European Molecular Biology Laboratory (EMBL), who helped develop AlphaFold with DeepMind, added that it was “remarkable” that the whole protein universe is now available in one or just two clicks.

“This will inspire many researchers around the world to think about what experiments they could do,” he said.

AlphaFold has been touted as one of the greatest scientific advancements of recent years and has the potential to revolutionize various fields including pharmacology, agronomy and vaccine manufacturing. It is also used to tackle the existential issues of plastic pollution and antibiotic resistance.

A major avenue that is aided by AlphaFold’s technological acumen is that of disease treatment.

Scientists from Duke University and the National University of Singapore published a paper in May based on the results made possible by AlphaFold.

They focused on a protein called phosphoprotein 1 (STIP1) which they were able to identify as something that helps protect the brain but is targeted and destroyed by the immune system of people with Parkinson’s disease.

Until now, the structure of this protein was never known in detail and AlphaFold was able to accurately predict the structure from the DNA and amino acid arrangement of the protein.

This, the researchers said, was “in excellent agreement” with the fuzzier picture of the protein obtained through experiments.

By enabling researchers to overcome their technological and laboratory obstacles, AlphaFold has elevated nearly every field of biology. This is a watershed moment for the life sciences and it will reap rewards in many different fields in the years to come.

“AlphaFold has been transformational”

Professor Matt Higgins, professor of molecular parasitology at the University of Oxford, is using AlphaFold to fight malaria by creating new vaccines against the mosquito-borne parasite.

His protein of interest has always been “fuzzy,” despite years of lab work, he said.

“Using AlphaFold has been truly transformational, giving us a very clear view of this maaria surface protein,” said Professor Higgins.

This has now led to the production of new candidate vaccines, and they are now being tested, Prof Higgins said.

“I’ve never seen anything like it”

“AlphaFold has sent ripples through the molecular biology community. In the past year alone, there have been over a thousand scientific papers on a wide range of research topics that utilize AlphaFold structures; I’ve never seen anything like it,” said Dr Sameer Velankar, team leader at the EMBL-EBI Protein Database in Europe.

“And that’s just the impact of a million predictions; imagine the impact of having over 200 million freely accessible protein structure predictions in the AlphaFold database.

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