Generative AI and Proteins

 Always an interest of mine, often mentioned here, approach should be interesting

Generative AI is dreaming up new proteins      by Laura Howes  in Cen.acs.org

April 10, 2023 | A version of this story appeared in Volume 101, Issue 12

In the past year, phrases like learned language models, diffusion, and hallucination have gained new meanings in popular culture as artificial intelligence has started taking over mundane tasks. Today, users can log on to an AI-powered chatbot and ask it to draft texts based on simple prompts. They can then use text-to-image services to create illustrations and new images to accompany the dreamed-up words.

But beyond these consumer applications, algorithmic approaches are helping researchers create a whole world of new proteins—proteins that could become vaccines, biologic therapies, materials, or tools for bioremediation.

A few years ago, C&EN chatted with David Baker of the University of Washington about a host of topics, including de novo protein design, which is designing new proteins from scratch rather than adjusting existing ones. Back then, he said he tried not to look too far into the future. Too much could change; too much was uncertain. That has never been truer.

De novo protein design has reached an inflection point, researchers say. AI-powered protein design is becoming very real and very usable, thanks to technological advances in the development of algorithms and the hardware that runs them.

Protein science itself was uniquely positioned to take advantage of these advances because of the enormous amounts of work carried out over the past 50 years to curate and annotate biological data.

“Every time there is a new method in computer vision or natural language processing, we are in a race to try to transfer it to biology,” says protein designer Noelia Ferruz at the Institute of Molecular Biology of Barcelona. “I guess it’s the perfect moment, because we’re seeing an AI revolution in every field.”

THE PROTEIN DESIGN PUZZLE

Proteins are hugely variable and incredibly specialized. They can form large, complicated complexes that mediate biological functions, or they can exist as small peptides that merely send signals from place to place. Proteins move and interact. They bind to and modify one another. They form part of the complex molecular dance we call life.

But proteins are also just molecules. They are composed of amino acid building blocks stuck together using amide linkages to create polymer chains. These polymers can curl up to build various shapes, chemical environments, forms, and functions, depending on where they sit and the interactions between the side chains in the molecules. For example, a hydrophobic portion might be found curled up inside the protein it’s part of or buried in a fatty membrane.  ... '