Publications associées à Targeting protein-ligand neosurfaces with a generalizable deep learning tool

Publications associées (10)

Programmable supramolecular nanoarchitectures for targeting biological patterns

Intricate spatial organization is omnipresent in biological systems across molecular, cellular, and tissue scales and has significant implications for health and disease. Biological patterns arise from complex molecular interactions and gradients, which, r ...

EPFL2025

Deep Neural Networks: Large-Width Behavior and Generalization Bounds

Evgenii Golikov

During several decades, neural network architectures have undergone considerable evolution: from shallow to deep, from fully connected to structured (e.g. convolutional, recurrent, or residual), from unnormalized to normalized. The present thesis contribut ...

EPFL2025

PeSTo-Carbs: Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces

Parth Bibekar, Matteo Dal Peraro, Lucien Fabrice Krapp

The Protein Structure Transformer (PeSTo), a geometric transformer, has exhibited exceptional performance in predicting protein-protein binding interfaces and distinguishing interfaces with nucleic acids, lipids, small molecules, and ions. In this study, w ...

Amer Chemical Soc2024

TMX5/TXNDC15, a natural trapping mutant of the PDI family is a client of the proteostatic factor ERp44

Maurizio Molinari

The ER is the organelle of nucleated cells that produces lipids, sugars, and proteins. More than 20 ER-resident members of the protein disulfide isomerase (PDI) family regulate formation, isomerization, and disassembly of covalent bonds in newly synthesize ...

LIFE SCIENCE ALLIANCE LLC2024

Predicting chemical hazard across taxa through machine learning

Kristin Schirmer, Julita Maria Stadnicka-Michalak

We applied machine learning methods to predict chemical hazards focusing on fish acute toxicity across taxa. We analyzed the relevance of taxonomy and experimental setup, showing that taking them into account can lead to considerable improvements in the cl ...

PERGAMON-ELSEVIER SCIENCE LTD2022

Semiaromatic Polyamides with Re-Entrant Chain Folding Templated by "U-Turn" Repeat Units

Rosario Scopelliti, Farzaneh Fadaei Tirani, John Christopher Plummer, Holger Frauenrath, Bilal Özen, Julien Philippe Cretenoud, Michael Alan Giffin

Biopolymers often show deterministic chain folding templated by repeat unit sequences whose conformations are locked in by intramolecular interactions. In this work, we have used repeat units based on rigid anthracene or acridine scaffolds, which we refer ...

American Chemical Society2021

Orientation, rotation and solvation of ions in helium nanodroplets

Verónica Oliver Álvarez de Lara

Helium nanodroplets are liquid, finite size, nanoscale helium clusters that have been employed since the 1990s as a matrix for high-resolution spectroscopy of molecules. Spectroscopic studies of ionic species inside helium droplets were not however realise ...

EPFL2019

Cu Photoredox Catalysts Supported by a 4,6-Disubstituted 2,2 '-Bipyridine Ligand: Application in Chlorotrifluoromethylation of Alkenes

Xile Hu, Murat Alkan

Interest in base metal catalysis motivates the development of Cu-based photoredox catalysts for organic synthesis. However, only a few Cu catalysts have been applied in photoredox reactions, the majority of which contain one or two 1,10-phenanthroline liga ...

2018

Molecular insights in aqueous systems : from electrolyte solutions to aqueous nanoscale interfaces

Yixing Chen

The unique structure and dynamics of the water hydrogen (H)-bond network enable a multitude of structures and chemical reactions in both bulk solutions and at interfaces. The underlying molecular interactions between water and dissolved electrolytes, organ ...

EPFL2017

Small-Molecule Adsorption in Open-Site Metal-Organic Frameworks: A Systematic Density Functional Theory Study for Rational Design

Berend Smit

Using density functional theory, we systematically compute and investigate the binding enthalpies of 14 different small molecules in a series of isostructural metalorganic frameworks, M-MOF-74, with M = Mg, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, and Zn. The small ...

American Chemical Society2015