Publication

Opportunities and challenges in design and optimization of protein function

Publications associées (98)

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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 ...
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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

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

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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 SCIENCE2023

First paleoproteome study of fossil fish otoliths and the pristine preservation of the biomineral crystal host

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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 ...
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Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

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The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikati ...
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Motifs for making tricycles

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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 PORTFOLIO2023

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Zander Harteveld

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 ...
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Deep learning approaches for conformational flexibility and switching properties in protein design

Patrick Daniel Barth, Mahdi Hijazi

Following the hugely successful application of deep learning methods to protein structure prediction, an increasing number of design methods seek to leverage generative models to design proteins with improved functionality over native proteins or novel str ...
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Proteins are the basic building blocks necessary for the operation and regulation of virtually all functions in living organisms. Over millions of years, evolution has created a vast repertoire of proteins finely tuned to execute their biological functions ...
EPFL2022

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Anne-Florence Raphaëlle Bitbol

Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...
NATURE PORTFOLIO2022

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