D. Baker

Hierarchical design of multi-scale protein complexes by combinatorial assembly of oligomeric helical bundle and repeat protein building blocks

This paper describes a hierarchical method to design multi-scale symmetric protein complexes using repeat proteins and helical bundles, resulting in large symmetric assemblies like an icosahedral nanocage.

Protein sequence design by explicit energy landscape optimization

This paper designs protein sequences by optimizing an energy landscape to ensure they fold into a desired structure, showing improved performance over traditional methods.

De novo protein design by deep network hallucination

The paper uses deep networks to design new proteins by inverting structure prediction models, resulting in 27 stable folded proteins with diverse structures.

Elicitation of broadly protective immunity to influenza by multivalent hemagglutinin nanoparticle vaccines

Nanoparticle immunogens with four seasonal influenza hemagglutinins elicit neutralizing antibodies against both the head and stem, providing broad protection against diverse influenza strains.

Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM

This paper uses deep learning and computational methods to determine an almost-complete atomic model of the Fanconi Anemia core complex from a low-resolution cryoEM map.

The genomes of invasive coral Tubastraea spp. (Dendrophylliidae) as tool for the development of biotechnological solutions

This paper presents three genomes of invasive coral Tubastraea spp. and identifies genomic features related to invasiveness and immunity, providing insights for biotechnological applications in coral management.

A generative algorithm for de novo design of proteins with diverse pocket structures

This paper introduces a generative algorithm for designing de novo proteins with diverse small molecule binding pockets, validated through experimental testing and showing improved stability and diversity compared to natural proteins.

Targeting HIV Env immunogens to B cell follicles in non-human primates through immune complex or protein nanoparticle formulations

This study shows that HIV Env immunogens can be concentrated in B cell follicles using immune complexes or protein nanoparticles, enhancing their localization in lymph nodes and potentially improving immune responses.

Structural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens

The paper evaluates de novo-designed two-component nanoparticles for presenting HIV Env trimers, showing improved antibody responses through multivalent display.

Computational design of a protein family that adopts two well-defined and structurally divergent de novo folds

This paper designs a protein family with two structurally divergent folds, showing that sequences can adopt distinct conformations under different conditions.

Antibody Targeting of B7-H4 Enhances the Immune Response in Urothelial Carcinoma

This study identifies B7-H4 as a potential therapeutic target in bladder cancer, showing that anti-B7-H4 antibodies enhance immune responses and reduce tumor size in preclinical models.

Antibody responses to Zika virus protein in pregnant and non-pregnant macaques

This study profiles anti-ZIKV antibody reactivity in macaques and shows that ZIKV-specific responses can wane over time and may be confused with DENV cross-reactivity.

The Rosetta all-atom energy function for macromolecular modeling and design

The paper explains the Rosetta all-atom energy function, its mathematical models, and its application to biomolecular modeling and design, including new capabilities for membrane proteins and other macromolecules.

Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration

The paper shows that integrin orientation is dictated by actin flow direction and cytoskeletal forces during leukocyte migration.