Basile I. M. Wicky

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.

De novo design of a macrocycle induced dimerization system for cellular control

This paper designs a chemically induced dimerization system using a de novo macrocycle and protein homodimer to control cellular processes.

Large-scale exploration of protein space by automated NMR

This paper develops a scalable NMR pipeline to characterize protein structure and dynamics, finding that designed proteins adopt intended folds and exhibit unexpected dynamics not captured by current models.

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.

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.

Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding

The paper develops a method to assess solution properties of designed proteins using mass spectrometry and peptide barcoding, enabling analysis of large protein libraries.

Hallucination of closed repeat proteins containing central pockets

The paper designs closed repeat proteins with central pockets using deep learning and validates them in E. coli, showing structural consistency and potential for small molecule binding.

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.

A Generative Model for Creating Path Delineated Helical Proteins

This paper introduces a generative model to design helical proteins by assembling helix fragments guided by a GAN architecture, enabling rapid and computationally efficient scaffold generation.

Language models generalize beyond natural proteins

A sequence-only protein language model, sampled under a structure-compatibility energy, produced designs of which 152 of 228 tested behaved as soluble monomers, some with no detectable UniRef90 match.

Detection of antibodies neutralizing historical and emerging SARS-CoV-2 strains using a thermodynamically coupled de novo biosensor system

The paper introduces a thermodynamically coupled biosensor to rapidly detect neutralizing antibodies against SARS-CoV-2 strains in serum samples.

Reconfigurable asymmetric protein assemblies through implicit negative design

This paper designs reconfigurable asymmetric protein assemblies using implicit negative design principles, enabling stable subunit exchange and diverse complex formations.