Publication
Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design
Publications associées (82)
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 ...
Cambridge2023De 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 ...
2023Generative power of a protein language model trained on multiple sequence alignments
Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo
Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...
eLIFE SCIENCES PUBL LTD2023Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins
Anne-Florence Raphaëlle Bitbol
Author summaryWhen two protein families interact, their sequences feature statistical dependencies. First, interacting proteins tend to share a common evolutionary history. Second, maintaining structure and interactions through the course of evolution yiel ...
PUBLIC LIBRARY SCIENCE2023Systems and methods for de novo design of protein interactions with learned surface fingerprints
Michael Bronstein, Pablo Gainza Cirauqui, Zander Harteveld, Andreas Scheck, Anthony Marchand, Sarah Wehrle, Freyr Sverrisson, Alexandra Krina Van Hall-Beauvais
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 ...
2023Computer-implemented design of peptide:receptor signaling complexes for enhanced chemotaxis
Patrick Daniel Barth, Robert Everett Jefferson
The present invention relates to a computer-implemented method for engineering the interaction between a protein and a cognate peptide that are capable of forming a molecular complex, wherein the method comprises (a) preparing in silico a library of test p ...
2023Rational Design of Chemically Controlled Antibodies and Protein Therapeutics
Li Tang, Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Pablo Gainza Cirauqui, Anthony Marchand, Leo Scheller, Lucia Bonati, 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 ...
2023Difference in astringency of the main pea protein fractions
Francesco Stellacci, Hanna Fanny Clarisse Lesme
Interactions between food and saliva govern complex mouthfeel perceptions such as astringency. Herein, we present a study of the interactions of salivary proteins with the main pea protein fractions that are obtained by isoelectric and salt precipitation ( ...
London2023Motifs for making tricycles
Tricyclic peptides have reduced conformational flexibility, making them well suited for ligand development. Researchers have now generated large combinatorial libraries of tricyclic peptides using a disulfide-directing motif. Screening these libraries disc ...
NATURE PORTFOLIO2023Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions
The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...
EPFL2022