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Showing posts with label Proteins. Show all posts
Showing posts with label Proteins. Show all posts

Saturday, September 3, 2022

‘The entire protein universe’: AI predicts shape of nearly every known protein

Ewen Callaway
Nature (608)
Posted with correction 29 July 22

From today, determining the 3D shape of almost any protein known to science will be as simple as typing in a Google search.

Researchers have used AlphaFold — the revolutionary artificial-intelligence (AI) network — to predict the structures of more than 200 million proteins from some 1 million species, covering almost every known protein on the planet.

The data dump is freely available on a database set up by DeepMind, the London-based AI company, owned by Google, that developed AlphaFold, and the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL–EBI), an intergovernmental organization near Cambridge, UK.

“Essentially you can think of it covering the entire protein universe,” DeepMind chief executive Demis Hassabis said at a press briefing. “We’re at the beginning of a new era of digital biology.”

The 3D shape, or structure, of a protein is what determines its function in cells. Most drugs are designed using structural information, and the creation of accurate maps of proteins’ amino-acid arrangement is often the first step to making discoveries about how proteins work.

DeepMind developed the AlphaFold network using an AI technique called deep learning, and the AlphaFold database was launched a year ago with more than 350,000 structure predictions covering nearly every protein made by humans, mice and 19 other widely studied organisms. The catalogue has since swelled to around 1 million entries.

“We’re bracing ourselves for the release of this huge trove,” says Christine Orengo, a computational biologist at University College London, who has used the AlphaFold database to identify new families of proteins. “Having all the data predicted for us is just fantastic.”

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But such entries tend to be skewed toward human, mouse and other mammalian proteins, Porta says. It’s likely that the AlphaFold dump will add significant knowledge, because it includes such a diverse range of organisms. “It’s going to be an awesome resource. And I’m probably going to download it as soon as it comes out,” says Porta.

Monday, April 24, 2017

Scientists Hack a Human Cell and Reprogram it Like a Computer

Sophia Chen
Wired Magazine
Originally published March 27, 2017

CELLS ARE BASICALLY tiny computers: They send and receive inputs and output accordingly. If you chug a Frappuccino, your blood sugar spikes, and your pancreatic cells get the message. Output: more insulin.

But cellular computing is more than just a convenient metaphor. In the last couple of decades, biologists have been working to hack the cells’ algorithm in an effort to control their processes. They’ve upended nature’s role as life’s software engineer, incrementally editing a cell’s algorithm—its DNA—over generations. In a paper published today in Nature Biotechnology, researchers programmed human cells to obey 109 different sets of logical instructions. With further development, this could lead to cells capable of responding to specific directions or environmental cues in order to fight disease or manufacture important chemicals.

Their cells execute these instructions by using proteins called DNA recombinases, which cut, reshuffle, or fuse segments of DNA. These proteins recognize and target specific positions on a DNA strand—and the researchers figured out how to trigger their activity. Depending on whether the recombinase gets triggered, the cell may or may not produce the protein encoded in the DNA segment.

The article is here.