Publications by Andreas Scheck

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

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

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

Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation

Jacques Fellay, Dylan Lawless, Olivier Noël Marie Naret, Andreas Scheck, Zhi Ming Xu, Arne Schneuing

Evolutionary changes in the hepatitis B virus (HBV) genome could reflect its adaptation to host -induced selective pressure. Leveraging paired human exome and ultra -deep HBV genome-sequencing data from 567 affected individuals with chronic hepatitis B, we ...

Cell Press2024

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

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

WILEY2023

De novo design of protein interactions with learned surface fingerprints

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Charlène Mireille Raymonde Raclot, Sandrine Madeleine Suzanne Georgeon, Beat Fierz, Aaron Simone Petruzzella, Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Stéphane Rosset, Alexandra Krina Van Hall-Beauvais, Alexandra Teslenko, Jane Marsden, Michael Bronstein, Casper Alexander Goverde, Stephen Michael Buckley, Dongchun Ni, Martin Pacesa

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

Systems and methods for de novo design of protein interactions with learned surface fingerprints

Anthony Marchand, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Alexandra Krina Van Hall-Beauvais, Michael Bronstein

The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...

2023

RosettaSurf-A surface-centric computational design approach

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

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

Computational design of vaccine immunogens

Bruno Emanuel Ferreira De Sousa Correia, Andreas Scheck, Karla Montserrat Castro Gilabert, Shuhao Xiao

Computational protein engineering has enabled the rational design of customized proteins, which has propelled both sequence-based and structure-based immunogen engineering and delivery. By discerning antigenic determinants of viral pathogens, computational ...

CURRENT BIOLOGY LTD2022

On the exploration of novel methodological approaches for immunogen design: case studies in influenza and hepatitis C

Andreas Scheck

Proteins are fundamental components in biological systems and crucial for a variety of biological functions. Over the last decades, significant progress in structural biology has facilitated the study of proteins and their interactions with molecular partn ...

EPFL2021

De Novo Design of Site-specific Protein Binders Using Surface Fingerprints

Sandrine Madeleine Suzanne Georgeon, Aaron Simone Petruzzella, Elisa Oricchio, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Stéphane Rosset, Alexandra Krina Van Hall-Beauvais

WILEY2021

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Thomas Huber, Lei Shi, Andreas Scheck, Patrick Daniel Barth, Hamed Khakzad, Alisa Khramushin

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and ...

NATURE PUBLISHING GROUP2020

Computational design of anti-CRISPR proteins with improved inhibition potency

Wei Sun, Sandrine Madeleine Suzanne Georgeon, Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Andreas Scheck, Stéphane Rosset, Julius Valten Upmeier Zu Belzen, Yujia Wang

Anti-CRISPR (Acr) proteins are powerful tools to control CRISPR-Cas technologies. However, the available Acr repertoire is limited to naturally occurring variants. Here, we applied structure-based design on AcrIIC1, a broad-spectrum CRISPR-Cas9 inhibitor, ...

NATURE PUBLISHING GROUP2020

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics

Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Jaume Bonet Martinez, Fabian Sesterhenn, Andreas Scheck

BackgroundLarge-scale datasets of protein structures and sequences are becoming ubiquitous in many domains of biological research. Experimental approaches and computational modelling methods are generating biological data at an unprecedented rate. The deta ...

2019

Rosetta FunFolDes - A general framework for the computational design of functional proteins

Bruno Emanuel Ferreira De Sousa Correia, Anne Marie-Thérèse Suzanne Billet, Jaume Bonet Martinez, Fabian Sesterhenn, Che Yang, Sabrina Susan Vollers, Freyr Sverrisson, Mélanie Evelyne Villard, Andreas Scheck, Sarah Wehrle, Roxanne Marine Lourman, Stéphane Rosset, Karen Schriever

The robust computational design of functional proteins has the potential to deeply impact translational research and broaden our understanding of the determinants of protein function and stability. The low success rates of computational design protocols an ...

2018