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Deep learning reveals how proteins interact

A team led by scientsts in the Baker lab has combined recent advances in evolutionary analysis and deep learning to build three-dimensional models of how most proteins in eukaryotes interact. This breakthrough has significant implications for understanding the biochemical processes common to all animals, plants, and fungi. This open-access work appears in Science. “To really …

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Accurate protein structure prediction accessible to all

Today we report the development and initial applications of RoseTTAFold, a software tool that uses deep learning to quickly and accurately predict protein structures based on limited information. Without the aid of such software, it can take years of laboratory work to determine the structure of just one protein. With RoseTTAFold, a protein structure can be …

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Hitching a ride into the brain

In a new paper, we describe a general approach for designing proteins that bind to exposed polar backbone groups at the edge of beta sheets with geometrically matched beta strands. We used this approach to create small proteins that bind to an exposed beta sheet on the human transferrin receptor, which shuttles interacting proteins across …

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Designed proteins assemble antibodies into modular nanocages

This week we report the design of new proteins that cluster antibodies into dense particles, rendering them more effective. In laboratory testing, such clustered antibodies neutralize COVID-19 pseudovirus, enhance cell signaling, and promote the growth of T cells more effectively than do free antibodies. This new method for enhancing antibody potency may eventually be used …

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A deep learning approach to protein design

Together with scientists at the Ovchinnikov lab at Harvard, we have applied deep learning to the challenge of protein design, yielding a new way to quickly create protein sequences that fold up as desired. This breakthrough has broad implications for the development of protein-based medicines and vaccines. Computational protein design has primarily focused on finding amino acid …

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De novo design of transmembrane beta barrels

  In a milestone for biomolecular design, a team of scientists has succeeded in creating new proteins that adopt one of the most complex folds known to molecular biology. These designer proteins were shown in the lab to spontaneously fold into their intended structures and embed into lipid membranes. Appearing in the journal Science [PDF], …

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De novo design of modular protein biosensors

This week we report [PDF] a new way to detect the virus that causes COVID-19, as well as antibodies against it. We have created protein-based sensors that glow when mixed with components of the virus or specific antibodies. This breakthrough could enable faster and more widespread testing in the near future. To directly detect key proteins that make up …

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Biologically active 2D arrays

Today we report the design of a new class of protein material that interacts with living cells without being absorbed by them. These large, flat arrays built from multiple protein parts can influence cell signaling by clustering and anchoring cell surface receptors. This breakthrough could have far-reaching implications for stem cell research and enable the …

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De novo minibinders target SARS-CoV-2 Spike protein

Today we report in Science [PDF] the design of small proteins that protect cells from SARS-CoV-2, the virus that causes COVID-19. In experiments involving lab-grown human cells, the activity of the lead antiviral candidate produced (LCB1) was found to rival that of the best-known SARS-CoV-2 neutralizing antibodies. LCB1 is currently being evaluated in rodents. This …

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