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Showing 1–26 of 26 results
Advanced filters: Author: Asim K. Bera Clear advanced filters

  • A generative artificial intelligence-powered method enables de novo design of highly active enzymes based on information about the geometry of residues in the active site, without requiring protein backbone or sequence information.

    • Donghyo Kim
    • Seth M. Woodbury
    • David Baker
    ResearchOpen Access
    Nature
    Volume: 649, P: 246-253

  • A fresh approach to protein design that incorporates excited intermediate states enables precise control over the lifetime of protein interactions, with potential applications in cell-signalling modulation and in biosensors and synthetic circuits.

    • Adam J. Broerman
    • Christoph Pollmann
    • David Baker
    ResearchOpen Access
    Nature
    Volume: 647, P: 528-535

  • A method for de novo design of peptide macrocyles called RFpeptides has been developed. RFpeptides is an extension of RoseTTAFold2 and RFdiffusion and combines structure prediction and protein backbone generation for rapid and custom design of macrocyclic peptide binders.

    • Stephen A. Rettie
    • David Juergens
    • Gaurav Bhardwaj
    ResearchOpen Access
    Nature Chemical Biology
    Volume: 21, P: 1948-1956

  • Immune receptors regulate immune responses and are key cancer immunotherapy targets. Here, the authors designed helical concave scaffolds to bind convex sites in immune receptors, creating high-affinity protein binders for TGFβRII, CTLA-4, and PD-L1. Co-crystal structures confirmed their therapeutic potential.

    • Wei Yang
    • Derrick R. Hicks
    • David Baker
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-12

  • A de novo-designed protein that precisely assembles a chlorophyll dimer has been developed. The design matches the conformation of the native ‘special pair’ of chlorophylls that functions as the primary electron donor in natural photosynthetic reaction centers. In the designed protein, excitonically coupled chlorophylls participate in energy transfer. The proteins were also redesigned to assemble into 24-chlorophyll nanocages.

    • Nathan M. Ennist
    • Shunzhi Wang
    • David Baker
    ResearchOpen Access
    Nature Chemical Biology
    Volume: 20, P: 906-915

  • Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible antivenom treatments.

    • Susana Vázquez Torres
    • Melisa Benard Valle
    • David Baker
    ResearchOpen Access
    Nature
    Volume: 639, P: 225-231

  • AfCycDesign: Cyclic offset to the relative positional encoding in AlphaFold2 enables accurate structure prediction, sequence redesign, and de novo hallucination of cyclic peptide monomers and binders.

    • Stephen A. Rettie
    • Katelyn V. Campbell
    • Gaurav Bhardwaj
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-15

  • A design pipeline is presented whereby binding proteins can be designed de novo without the need for prior information on binding hotspots or fragments from structures of complexes with binding partners.

    • Longxing Cao
    • Brian Coventry
    • David Baker
    ResearchOpen Access
    Nature
    Volume: 605, P: 551-560

  • The trRosetta neural network was used to iteratively optimise model proteins from random 100-amino-acid sequences, resulting in ‘hallucinated’ proteins, which when expressed in bacteria closely resembled the model structures.

    • Ivan Anishchenko
    • Samuel J. Pellock
    • David Baker
    Research
    Nature
    Volume: 600, P: 547-552

  • A study describes an approach using designed building blocks that are far more regular in geometry than natural proteins to construct modular multicomponent protein assemblies.

    • Timothy F. Huddy
    • Yang Hsia
    • David Baker
    ResearchOpen Access
    Nature
    Volume: 627, P: 898-904

  • Roy et al. describe a generalized method for computationally designing miniproteins selective for a single integrin heterodimer and conformational state. The designed αvβ6 inhibitor remains monomeric and maintains biological activity following aerosolization and shows excellent efficacy in bleomycin induced lung fibrosis.

    • Anindya Roy
    • Lei Shi
    • David Baker
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-18

  • Most proteins mediating biomineralization in nature are not well structured, and the structures of the relevant protein-mineral interfaces regulating mineralization are elusive. Here, the authors computationally design proteins that modulate calcium carbonate mineralization to generate hybrid materials and elucidate the roles of designed proteins in controlling mineralization.

    • Fatima A. Davila-Hernandez
    • Biao Jin
    • David Baker
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-11

  • An approach to design proteins that can capture amyloidogenic protein regions present in, for example, tau and Aβ42 has now been developed. These designer proteins can inhibit the formation of pathogenic amyloid fibrils and protect cells from toxic species.

    • Danny D. Sahtoe
    • Ewa A. Andrzejewska
    • David Baker
    ResearchOpen Access
    Nature Chemical Biology
    Volume: 20, P: 981-990

  • Here, the authors constructed a deep-learning approach to design closed repeat proteins with central binding pockets—a step towards designing proteins to specifically bind small molecules.

    • Linna An
    • Derrick R. Hicks
    • David Baker
    ResearchOpen Access
    Nature Structural & Molecular Biology
    Volume: 30, P: 1755-1760

  • Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be lengthened or shortened by changing the length of the monomers. Now a systematic approach to generate modular repeat protein oligomers with combined symmetry that can be extended by repeat propagation has been developed.

    • Neville P. Bethel
    • Andrew J. Borst
    • David Baker
    ResearchOpen Access
    Nature Chemistry
    Volume: 15, P: 1664-1671

  • The process of protein crystallization is poorly understood and difficult to program through the primary sequence. Here the authors develop a computational approach to designing three-dimensional protein crystals with prespecified lattice architectures with high accuracy.

    • Zhe Li
    • Shunzhi Wang
    • David Baker
    Research
    Nature Materials
    Volume: 22, P: 1556-1563

  • The authors use computational protein design to stabilize the active conformation of cGAS, generating constitutively active cGAS variants that could potentiate prophylactic and therapeutic effects.

    • Quinton M. Dowling
    • Hannah E. Volkman
    • Neil P. King
    Research
    Nature Structural & Molecular Biology
    Volume: 30, P: 72-80

  • Cyclic peptides are of particular interest due to their pharmacological properties, but their design for binding to a target protein is challenging. Here, the authors present a computational “anchor extension” methodology for de novo design of cyclic peptides that bind to the target protein with high affinity, and validate the approach by developing cyclic peptides that inhibit histone deacetylases 2 and 6.

    • Parisa Hosseinzadeh
    • Paris R. Watson
    • David Baker
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-12

  • De novo design of self-assembling protein nanostructures and materials is of significant interest, however design of complex, multi-component assemblies is challenging. Here, the authors present a stepwise hierarchical approach to build such assemblies using helical repeat and helical bundle proteins as building blocks, and provide an in-depth structural characterization of the resulting assemblies.

    • Yang Hsia
    • Rubul Mout
    • David Baker
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-10