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In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene

Publications associées (26)

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 th ...

EPFL2024

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

Computational drug development for membrane protein targets

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

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

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

Combining 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 SCIENCE2023

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Lucien Fabrice Krapp

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 ...

EPFL2023

Saliency prediction in 360° architectural scenes: Performance and impact of daylight variations

Marilyne Andersen, Sabine Süsstrunk, Caroline Karmann, Kynthia Chamilothori, Seungryong Kim, Bahar Aydemir

Saliency models are image-based prediction models that estimate human visual attention. Such models, when applied to architectural spaces, could pave the way for design decisions where visual attention is taken into account. In this study, we tested the pe ...

2023

DeepBreath-automated detection of respiratory pathology from lung auscultation in 572 pediatric outpatients across 5 countries

Martin Jaggi, Mary-Anne Hartley, Jonathan Dönz, Juliane Dervaux, Tatjana Chavdarova, Daniel Mueller, Julien Niklas Heitmann, Daniel Hinjos García

The interpretation of lung auscultation is highly subjective and relies on non-specific nomenclature. Computer-aided analysis has the potential to better standardize and automate evaluation. We used 35.9 hours of auscultation audio from 572 pediatric outpa ...

NATURE PORTFOLIO2023

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Andonis Samuel Rene Gerardos

Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families ...

Public Library Science2022

In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene

Predicting protein interactions using geometric deep learning on protein surfaces

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

Computational drug development for membrane protein targets

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

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

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Saliency prediction in 360° architectural scenes: Performance and impact of daylight variations

DeepBreath-automated detection of respiratory pathology from lung auscultation in 572 pediatric outpatients across 5 countries

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Graph Chatbot

Predicting protein interactions using geometric deep learning on protein surfaces

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

Computational drug development for membrane protein targets

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

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

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Machine-learned interatomic potentials: Recent developments and prospective applications

Saliency prediction in 360° architectural scenes: Performance and impact of daylight variations

DeepBreath-automated detection of respiratory pathology from lung auscultation in 572 pediatric outpatients across 5 countries

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Machine-learned interatomic potentials: Recent developments and prospective applications