Publications by Casper Alexander Goverde

Computational design of complex protein folds and soluble analogs of membrane proteins

Proteins are the molecular machines of life, driving essential biological processes such as enzymatic catalysis, cellular signaling, and immune responses. The ability to design entirely new proteins with desired structures and functions has immense implica ...

EPFL2025

An atlas of protein homo-oligomerization across domains of life

Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Casper Alexander Goverde, Martin Pacesa, Yoan Désiré Duhoo

Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalabl ...

2024

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

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

Structures of the Foamy virus fusion protein reveal an unexpected link with the F protein of paramyxo- and pneumoviruses

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

Foamy viruses (FVs) constitute a subfamily of retroviruses. Their envelope (Env) glycoprotein drives the merger of viral and cellular membranes during entry into cells. The only available structures of retroviral Envs are those from human and simian immuno ...

2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

Machine Learning in Protein Science De Novo Design of Site-Specific Protein Binders Using Surface Fingerprints

Didier Trono, Henning Paul-Julius Stahlberg, Priscilla Turelli, Bruno Emanuel Ferreira De Sousa Correia, Dongchun Ni, Andreas Scheck, Anthony Marchand, Casper Alexander Goverde, Pablo Gainza Cirauqui, Zander Harteveld

WILEY2023

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 new age in protein design empowered by deep learning

Bruno Emanuel Ferreira De Sousa Correia, Michael Bronstein, Hamed Khakzad, Casper Alexander Goverde, Arne Schneuing, Ilia Igashov

The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

Cell Press2023