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Bruno Emanuel Ferreira De Sousa Correia

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Publications associées (179)

Virucidal compounds and use thereof

Francesco Stellacci, Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui, Corey Alfred Stevens, Lukasz Richter, Francesca Olgiati, Chiara Medaglia

Disclosed herein are peptide-grafted compounds that irreversibly deactivate bacteriophages or influenza virus depending on the peptide and remain safe for bacteria and mammalian cells. The active compounds comprise a core (cyclodextrin or gold nanoparticle ...

2024

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

Rational Design of Chemically Controlled Antibodies and Protein Therapeutics

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

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

Track: Machine Learning in Protein Science De Novo Design of Viral Epitope Mimetics with Non-Regular Structural Features

Jue Wang, Bruno Emanuel Ferreira De Sousa Correia, Karla Montserrat Castro Gilabert, Anastassia Andreevna Vorobieva

WILEY2023

Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Emmanuel Doram Levy, Xiao Wang

Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest ...

2023

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

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

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

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, Casper Alexander Goverde, Ilia Igashov, Arne Schneuing, Hamed Khakzad

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

Rules and mechanisms governing G protein coupling selectivity of GPCRs

Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui

G protein-coupled receptors (GPCRs) convert extracellular stimuli into intracellular signaling by coupling to heterotrimeric G proteins of four classes: Gi/o, Gq, Gs, and G12/13. However, our understanding of the G protein selectivity of GPCRs is incomplet ...

Cell Press2023

Rational design of small-molecule responsive protein switches

Bruno Emanuel Ferreira De Sousa Correia, Sailan Shui, Leo Scheller, Stephen Michael Buckley

Small-molecule responsive protein switches are powerful tools for controlling cellular processes. These switches are designed to respond rapidly and specifically to their inducer. They have been used in numerous applications, including the regulation of ge ...

2023

Protein-based bandpass filters for controlling cellular signaling with chemical inputs

Bruno Emanuel Ferreira De Sousa Correia, Sailan Shui, Leo Scheller

Biological signal processing is vital for cellular function. Similar to electronic circuits, cells process signals via integrated mechanisms. In electronics, bandpass filters transmit frequencies with defined ranges, but protein-based counterparts for cont ...

Nature Portfolio2023

Novel cathepsin inhibitors

Aaron Simone Petruzzella, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio

The present invention relates to a cathepsin inhibitor comprising or consisting of Formula (I) (X1)(X2)(X3)(X4)(Y)(X5)(X6)(X7) wherein (X1) is an amino acid selected from K, L, F and M; (X2) is an amino acid selected from L, A, D, E, F, G, H, I, K, M, N, S ...

2023

Scaffolding protein functional sites using deep learning

Basile Isidore Martin Wicky, Jue Wang, Bruno Emanuel Ferreira De Sousa Correia, Karla Montserrat Castro Gilabert, Wayne Yang Wen Wei

The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without needing ...

American Association for the Advancement of Science2022

Antibodies to combat viral infections: development strategies and progress

Bruno Emanuel Ferreira De Sousa Correia

Monoclonal antibodies (mAbs) are appealing as potential therapeutics and prophylactics for viral infections. This Review describes advances in antibody discovery and engineering that have led to the development of mAbs that target viruses such as severe ac ...

2022

Computational design of novel protein–protein interactions – An overview on methodological approaches and applications

Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Alexandra Krina Van Hall-Beauvais

Protein–protein interactions (PPIs) govern numerous cellular functions in terms of signaling, transport, defense and many others. Designing novel PPIs poses a fundamental challenge to our understanding of molecular interactions. The capability to robustly ...

2022

A method and system for fast end-to-end learning on protein surfaces

Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui, Freyr Sverrisson

The present invention concerns a computer-system-implemented method for predicting properties of a protein molecule, comprising the steps of: receiving an input representation of the protein molecule; applying a surface generator to produce a molecular sur ...

2022

A generic framework for hierarchical de novo protein design

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

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, Che Yang, Stéphane Rosset

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

Novel chemically controlled cellular switches

Bruno Emanuel Ferreira De Sousa Correia, Pablo Gainza Cirauqui, Sailan Shui

The invention relates to activation by inhibitor release (AIR) switches and chemically disruptable heterodimers (CDH), their use in controlling cell signaling components, and their use for treatments and therapies. ...

2022

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

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