Publications associées à Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures

Publications associées (39)

Boosting Protein Graph Representations through Static-Dynamic Fusion

Pengkang Guo, Pierre Vandergheynst, Bruno Emanuel Ferreira De Sousa Correia, Daniel Probst

Machine learning for protein modeling faces significant challenges due to proteins' inherently dynamic nature, yet most graph-based machine learning methods rely solely on static structural information. Recently, the growing availability of molecular dynam ...

2025

Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Aleksandar Antanasijevic

Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. For example, clathrin coats adopt a wide variety of architectures to adapt to vesicular cargos of various sizes. Although computational me ...

Nature Research2025

Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks

Patrick Daniel Barth, Lucas Sebastian Powell-Rudden

Protein catalysis and allostery require the atomic-level orchestration and motion of residues and ligand, solvent and protein effector molecules. However, the ability to design protein activity through precise protein–solvent cooperative interactions has n ...

Springer Science and Business Media LLC2025

Characterization of Machine Learning-Based Surrogate Models of Neural Activation Under Electrical Stimulation

Silvestro Micera, Simone Romeni

Bioelectromagnetics published by Wiley Periodicals LLC on behalf of Bioelectromagnetics Society.Electrical stimulation of peripheral nerves via implanted electrodes has been shown to be a promising approach to restore sensation, movement, and autonomic fun ...

2025

Role of S-acylating enzymes in ciliated cells

Daria Korotkova

S-acylation is a post-translational modification that can regulate protein localization, function, and turnover by reversible attachment of fatty acid to specific cysteine residues. It affects over 20% of proteins, with membrane proteins making up the larg ...

EPFL2025

Leaf Level Ash Dieback Disease Detection and Online Severity Estimation With UAVs

Mirko Kovac

Ash dieback, caused by the fungal pathogen Hymenoscyphus fraxineus, is devastating ash tree populations across U.K. and Europe, with projections indicating that up to 80% of ash trees may die as a result of the disease. The extensive loss of this keystone ...

2025

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

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 th ...

EPFL2024

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

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 ...

EPFL2024

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

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 ...

EPFL2024

Opportunities 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 Portfolio2024

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

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 ...

EPFL2024

Computational drug development for membrane protein targets

Pierre Vogel, Henning Paul-Julius Stahlberg, Shuguang Yuan, Dongchun Ni, Babatunde Edukpe Ekundayo

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

2024

Prolamins' 3D structure: A new insight into protein modeling using the language of numbers and shapes

Niloufar Sharif

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 Ltd2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Mohan Vamsi Nallapareddy, Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Simplification of spiking neural network models

Wulfram Gerstner, Henry Markram, Eilif Benjamin Muller, James Gonzalo King, Christian Antonio Pozzorini, Csaba Erö, Christian Andreas Rössert, Idan Segev, Willem Anna Mark Wybo

The simplification of neural network models is described. For example, a method for simplifying a neural network model includes providing the neural network model to be simplified, defining a first temporal filter for the conveyance of input from a neuron ...

2024

Deep learning approach for identification of H II regions during reionization in 21-cm observations - II. Foreground contamination

Jean-Paul Richard Kneib, Emma Elizabeth Tolley, Michele Bianco, Tianyue Chen

The upcoming Square Kilometre Array Observatory will produce images of neutral hydrogen distribution during the epoch of reionization by observing the corresponding 21-cm signal. However, the 21-cm signal will be subject to instrumental limitations such as ...

Oxford Univ Press2024

VDMNav: Software Architecture for Aerodynamically Constrained Navigation on Small Fixed-Wing Drones

Jan Skaloud, Aman Sharma, Gabriel François Laupré

Navigation of drones is predominantly based on sensor fusion algorithms. Most of these algorithms make use of some form of Bayesian filtering with a majority employing an Extended Kalman Filter (EKF), wherein inertial measurements are fused with a Global N ...

2024

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

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 ...

EPFL2024

Task-driven neural network models predict neural dynamics of proprioception: Experimental data, activations and predictions of neural network models

Alexander Mathis, Alberto Silvio Chiappa, Alessandro Marin Vargas, Axel Bisi

Here we provide the neural data, activation and predictions for the best models and result dataframes of our article "Task-driven neural network models predict neural dynamics of proprioception". It contains the behavioral and neural experimental data (cu ...

EPFL Infoscience2024