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Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins
Related publications (40)
Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions
Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...
EPFL2024Predicting protein interactions using geometric deep learning on protein surfaces
In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies.The first chapter introduces the ...
EPFL2024Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design
Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...
EPFL2024Opportunities and challenges in design and optimization of protein function
Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde
The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...
Nature Portfolio2024Prolamins' 3D structure: A new insight into protein modeling using the language of numbers and shapes
This study combined protein modeling methods to generate the prolamins' fractions as precise as possible. Hence, gliadins, zeins, kafirins, hordeins, secalins, avenins and oryzins were generated based on their characteristics and disulfide mapping. Finding ...
Elsevier Sci Ltd2024A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer
Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...
EPFL2023Generative 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 LTD2023A 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 designed proteins: a study in engineering novel folds and functions
Alexandra Krina Van Hall-Beauvais
Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...
EPFL2023De 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