Concept
Famille de protéines
Publications associées (98)
Generative 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 LTD2023First paleoproteome study of fossil fish otoliths and the pristine preservation of the biomineral crystal host
Anders Meibom, Jaroslaw Hubert Stolarski, Jinming Guo
Otoliths are calcium carbonate components of the stato-acoustical organ responsible for hearing and maintenance of the body balance in teleost fish. During their formation, control over, e.g., morphology and carbonate polymorph is influenced by complex ins ...
NATURE PORTFOLIO2023De 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 ...
2023Systems 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 ...
2023New protein–protein interactions designed by a computer
Pablo Gainza Cirauqui, Anthony Marchand
Creating protein interactions through computational design is a key challenge in the fields of both basic and translational biology. An approach that uses the machine-learned fingerprints of protein-surface features was used to produce synthetic proteins t ...
2023Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins
Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approa ...
NATURE PORTFOLIO2023A molecular device for the redox quality control of GroEL/ES substrates
Camille Véronique Bernadette Goemans
Hsp60 chaperonins and their Hsp10 cofactors assist protein folding in all living cells, constituting the paradigmatic example of molecular chaperones. Despite extensive investigations of their structure and mechanism, crucial questions regarding how these ...
2023Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences
Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Andonis Samuel Rene Gerardos
Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families ...
San Francisco2022Protein language models trained on multiple sequence alignments learn phylogenetic relationships
Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo
Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...
NATURE PORTFOLIO2022Assessing 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