Publications related to Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

Palladium-based supramolecular assemblies: from complex structures to water-soluble anion-receptors

The combination of palladium salts and bipyridyl ligands can lead to the formation of a large variety of coordination complexes, with different shapes and sizes, displaying a very versatile host-guest chemistry. Increasing their structural complexity remai ...

EPFL2024

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

Antenna-coupled infrared nanospectroscopy of intramolecular vibrational interaction

Hatice Altug, Aurélian Michel John-Herpin, Felipe Herrera

Many photonic and electronic molecular properties, as well as chemical and biochemical reactivities are controlled by fast intramolecular vibrational energy redistribution (IVR). This fundamental ultrafast process limits coherence time in applications from ...

National Academy of Sciences2023

Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors

Sarah Wehrle

Proteins are the basic building blocks necessary for the operation and regulation of virtually all functions in living organisms. Over millions of years, evolution has created a vast repertoire of proteins finely tuned to execute their biological functions ...

EPFL2022

Phase Reconstruction of Low-Energy Electron Holograms of Individual Proteins

Klaus Kern, Stephan Rauschenbach, Sven Alexander Szilagyi, Hannah Julia Ochner

Low-energy electron holography (LEEH) is one of the few techniques capable of imaging large and complex three-dimensional molecules, such as proteins, on the single molecule level at subnanometer resolution. During the imaging process, the structural infor ...

AMER CHEMICAL SOC2022

A universal workflow for creation, validation and generalization of detailed neuronal models

Henry Markram, Srikanth Ramaswamy, Mustafa Anil Tuncel, Werner Alfons Hilda Van Geit, Alexis Arnaudon, Christian Andreas Rössert, Maria Reva, Tanguy Pierre Louis Damart, Darshan Mandge

Detailed single neuron modeling is widely used to study neuronal functions. While cellular and functional diversity across the mammalian cortex is vast, most of the available computational tools are dedicated to the reproduction of a small set of specific ...

Cambridge2023

New Methods for the Integrative Dynamic Modeling of Biomolecular Structures

Sylvain Träger

The true understanding of most cellular functions is only really achievable through the structural determination of their underlying macromolecular assemblies. However, their size, large number of individual components and metastable states make their eluc ...

EPFL2021

Half-clathrochelate Complexes as Versatile Links in Supramolecular Chemistry

Erica Giraldi

Clathrochelate complexes have been widely investigated with different size and shape and used as building blocks for the obtainment of discrete supramolecular architectures. These clathrochelate complexes are very stable and kinetically inert complexes. A ...

EPFL2021

Fast end-to-end learning on protein surfaces

Bruno Emanuel Ferreira De Sousa Correia, Freyr Sverrisson

Proteins' biological functions are defined by the geometric and chemical structure of their 3D molecular surfaces. Recent works have shown that geometric deep learning can be used on mesh-based representations of proteins to identify potential functional s ...

IEEE COMPUTER SOC2021

Structural and analytical identifications of biomolecules by cold ion spectroscopy of non-covalent complexes

Erik Saparbayev

Non-covalent interactions are ubiquitous in nature. The diversity and functionality of these interactions are employed by nature as a universal tool for building the molecular mechanism of life. Although weak, these interactions play a key role in both for ...

EPFL2021