Robert J. Ragotte

Computational design of potent, broadly neutralizing anti-Nipah virus and Hendra virus miniproteins

This paper computationally designs thermostable miniproteins that neutralize Nipah and Hendra viruses with subnanomolar affinity and potent in vitro antiviral activity.

Accelerating protein design by scaling experimental characterization

This paper introduces scalable experimental and computational workflows to accelerate protein design by improving throughput, reducing costs, and enabling rapid validation of thousands of protein designs.

CF2H: a Cell-Free Two-Hybrid platform for rapid protein binder screening

CF2H is a cell-free two-hybrid platform that rapidly detects high-affinity protein-protein interactions without cloning or purification.

Atomically accurate de novo design of antibodies with RFdiffusion

This paper designs antibodies de novo with atomic precision using RFdiffusion and yeast display, validated by cryo-EM and biophysical methods.

De novo design of potent inhibitors of Clostridioides difficile toxin B

This paper designs potent small protein inhibitors of C. difficile toxin B using deep learning and Rosetta, showing high affinity and stability for potential clinical use.

Designed miniproteins potently inhibit and protect against MERS-CoV

This study designs miniproteins that inhibit MERS-CoV by targeting the spike protein, showing broad neutralization and protective efficacy in mice.

Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists

This study uses target-conditioned diffusion to design high-affinity TNFR superfamily antagonists and agonists with switchable specificity.

De novo designed inhibitor confers protection against lethal toxic shock

The paper designs a potent inhibitor against P. sordellii lethal toxin using deep learning, showing protective effects in mice against toxic shock.

Development of an improved blood-stage malaria vaccine targeting the essential RH5-CyRPA-RIPR invasion complex

This paper develops a combination malaria vaccine targeting the RCR-complex by fusing epitopes from RIPR to CyRPA, improving in vitro growth inhibition compared to RH5.1 alone.

Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models

Fine-tuning RoseTTAFold as a diffusion denoiser gives RFdiffusion, a general protein backbone generator; a designed influenza haemagglutinin binder matched its model by cryo-EM.