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Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

Publications associées (29)

Generative power of a protein language model trained on multiple sequence alignments

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Damiano Sgarbossa

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 LTD2023

Fast viral dynamics revealed by microsecond time-resolved cryo-EM

Marcel Drabbels, Ulrich Lorenz, Sarah Victoria Barrass, Oliver Florian Harder

Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incom- plete. To enable such observations, we have recently proposed a technique that improves the time resoluti ...

Nature Research2023

Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

Ghérici Hassaïne

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 Portfolio2023

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

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

Andreas Scheck, Michael Bronstein, Anthony Marchand, Pablo Gainza Cirauqui, Zander Harteveld, 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 ...

2023

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

Generative power of a protein language model trained on multiple sequence alignments

Fast viral dynamics revealed by microsecond time-resolved cryo-EM

Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

De novo design of protein interactions with learned surface fingerprints

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

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

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Graph Chatbot

Generative power of a protein language model trained on multiple sequence alignments

Fast viral dynamics revealed by microsecond time-resolved cryo-EM

Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

De novo design of protein interactions with learned surface fingerprints

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

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

Computer-implemented design of peptide:receptor signaling complexes for enhanced chemotaxis

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Computer-implemented design of peptide:receptor signaling complexes for enhanced chemotaxis