Concept
Protein–protein interaction prediction
Related publications (171)
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 ...
EPFL2024Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms
Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...
Wiley-V C H Verlag Gmbh2024Engineering 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 ...
EPFL2024Development of tools and methods for protein identification: From single molecules to in vivo applications.
As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...
EPFL2024Prolamins' 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 Ltd2024Investigating 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 ...
EPFL2024Dynamic Voxels Based on Ego-Conditioned Prediction: An Integrated Spatio-Temporal Framework for Motion Planning
Alexandre Massoud Alahi, Ting Zhang
Prediction is a vital component of motion planning for autonomous vehicles (AVs). By reasoning about the possible behavior of other target agents, the ego vehicle (EV) can navigate safely, efficiently, and politely. However, most of the existing work overl ...
Ieee-Inst Electrical Electronics Engineers Inc2024Combining 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 SCIENCE2023A 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 ...
EPFL2023Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins
Paolo De Los Rios, Alessandro Barducci, Mathieu Rebeaud, Stefano Zamuner, Duccio Malinverni
The 70-kD heat shock protein (Hsp70) chaperone system is a central hub of the proteostasis network that helps maintain protein homeostasis in all organisms. The recruitment of Hsp70 to perform different and specific cellular functions is regulated by the J ...
Washington2023