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New article in Nature: building 20,000 new drug candidates

In another major leap forward, researchers at the IPD have just published a revolutionary method for generating brand new protein drugs. These new drugs – called “mini-protein binders” – combine the specificity of antibodies with the high stability and manufacturability of small molecule drugs. The new de novo designed mini-protein binders were custom built to target either a …

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New article in Science: data-driven protein design

This summer saw a major advance in protein science: data-driven design. For decades, researchers have been trying to decode the rules of protein folding by studying how the complex, highly specialized proteins in nature hold their shapes. It’s a bit like trying to figure out how an airplane works – at its most fundamental level …

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Computational design of Flu Glue

Today, a multidisciplinary team of researchers at the University of Washington, Fred Hutch, and The Scripps Research Institute published in Nature Biotechnology the computational design of a trimeric influenza-neutralizing protein that binds extremely tightly to the H3 hemagglutinin of 1968 Hong Kong pandemic influenza virus (A/Hong Kong/X31/1968).   It also cross-reacts with human relevant H1, H2 …

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Protein structure determination using metagenome sequence data

Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number …

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Accurate design of megadalton-scale two-component icosahedral protein complexes

Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization …

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De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity

General design principles for protein interaction specificity are challenging to extract. In DNA, specificity arises from a limited set of hydrogen-bonding interactions in the core of the double helix to design and build a wide range of shapes. In proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Protein-based materials …

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