Publications de Stéphane Rosset

Exploring “dark-matter” protein folds using deep learning

Pierre Vandergheynst, Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Casper Alexander Goverde, Andreas Loukas, Stéphane Rosset, Zander Harteveld, Alexandra Krina Van Hall-Beauvais

De novo protein design explores uncharted sequence and structure space to generate novel proteins not sampled by evolution. A main challenge in de novo design involves crafting “designable” structural templates to guide the sequence searches toward adoptin ...

2024

A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins

Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset

Deep mutational scanning is a powerful method for exploring the mutational fitness landscape of proteins. Its adaptation to anti-CRISPR proteins, which are natural CRISPR-Cas inhibitors and key players in the co-evolution of microbes and phages, facilitate ...

2024

Epitope-focused immunogens targeting the hepatitis C virus glycoproteins induce broadly neutralizing antibodies

Bruno Emanuel Ferreira De Sousa Correia, Andreas Scheck, Stéphane Rosset, Sabrina Susan Vollers

Hepatitis C virus (HCV) infection causes similar to 290,000 annual human deaths despite the highly effective antiviral treatment available. Several viral immune evasion mechanisms have hampered the development of an effective vaccine against HCV, among the ...

AMER ASSOC ADVANCEMENT SCIENCE2024

Computational design of soluble and functional membrane protein analogues

Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Casper Alexander Goverde, Martin Pacesa, Stéphane Rosset

De novo design of complex protein folds using solely computational means remains a substantial challenge1. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, ...

2024

Rational Design of Chemically Controlled Antibodies and Protein Therapeutics

Li Tang, Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Anthony Marchand, Leo Scheller, Lucia Bonati, Pablo Gainza Cirauqui, Stéphane Rosset, Sailan Shui

Protein-based therapeutics, such as monoclonal antibodies and cytokines, are important therapies for various pathophysiological conditions such as oncology, autoimmune disorders, and viral infections. However, the wide application of such protein therapeut ...

2023

De novo design of protein interactions with learned surface fingerprints

Didier Trono, Henning Paul-Julius Stahlberg, Beat Fierz, Priscilla Turelli, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Sandrine Madeleine Suzanne Georgeon, Dongchun Ni, Andreas Scheck, Michael Bronstein

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

2023

De novo protein design by inversion of the AlphaFold structure prediction network

Bruno Emanuel Ferreira De Sousa Correia, Hamed Khakzad, Casper Alexander Goverde, Stéphane Rosset, Benedict Dieter Gregor Wolf

De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in comp ...

2023

A generic framework for hierarchical de novo protein design

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Fabian Sesterhenn, Zander Harteveld, Stéphane Rosset, Che Yang

De novo protein design enables the exploration of novel sequences and structures absent from the natural protein universe. De novo design also stands as a stringent test for our understanding of the underlying physical principles of protein folding and may ...

National Academy of Sciences2022

Assessing and enhancing foldability in designed proteins

Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset, Che Yang

Recent advances in protein-design methodology have led to a dramatic increase in reliability and scale. With these advances, dozens and even thousands of designed proteins are automatically generated and screened. Nevertheless, the success rate, particular ...

WILEY2022

RosettaSurf-A surface-centric computational design approach

Pierre Vandergheynst, Bruno Emanuel Ferreira De Sousa Correia, Andreas Scheck, Andreas Loukas, Jaume Bonet Martinez, Stéphane Rosset, Michaël Defferrard

Proteins are typically represented by discrete atomic coordinates providing an accessible framework to describe different conformations. However, in some fields proteins are more accurately represented as near-continuous surfaces, as these are imprinted wi ...

PUBLIC LIBRARY SCIENCE2022