Publication
Analytical Approaches for Monitoring DNA–Protein Interactions
Publications associées (38)
Predicting 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 ...
EPFL2024Investigating 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 ...
EPFL2024Microsecond Time-Resolved Cryo-Electron Microscopy
Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...
EPFL2024A 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 ...
Cambridge2023Generative 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 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 ...
EPFL2023Combining 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 SCIENCE2023Towards 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 ...
EPFL2022SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions
BackgroundStatistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we deco ...
BMC2021