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Publications associées (30)

Protein target highlights in CASP15: Analysis of models by structure providers

Bruno Lemaitre, Luciano Andres Abriata, Samuel Rommelaere, Kuan-Lin Wu, Han Xiao

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the su ...

WILEY2023

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

A generic framework for hierarchical de novo protein design

Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Jaume Bonet Martinez, Fabian Sesterhenn, Stéphane Rosset, Che Yang

De novo protein design enables the exploration of novel sequences and structures absent from the natural protein universe. De novo design also stands as a stringent test for our understanding of the underlying physical principles of protein folding and may ...

NATL ACAD SCIENCES2022

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez

Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant improv ...

AMER CHEMICAL SOC2021

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

Jaume Bonet Martinez

BackgroundStatistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we deco ...

BMC2021

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

Rigid foldability and mountain-valley crease assignments of square-twist origami pattern

Huijuan Feng

Rigid foldability allows an origami pattern to fold about crease lines without twisting or stretching component panels. It enables folding of rigid materials, facilitating the design of foldable structures. Recent study shows that rigid foldability is affe ...

PERGAMON-ELSEVIER SCIENCE LTD2020

A plane linkage and its tessellation for deployable structure

Huijuan Feng

Deployable structures are widely used in space applications such as solar arrays and antennas. Recently, inspired by origami, more deployable structures have been developed. This paper outlined a novel design scheme for deployable structures by taking a pl ...

PERGAMON-ELSEVIER SCIENCE LTD2019

A comparative study of earthquake source models in high- order accurate tsunami simulations

Jan Sickmann Hesthaven, Boris Bonev

The discontinuous Galerkin method is used to solve the non-linear spherical shallow water equations with Coriolis force. The numerical method is well-balanced and takes wetting/drying into account. The two fold goal of this work is a comparative study of d ...

2019

Low Fe(II) Concentrations Catalyze the Dissolution of Various Fe(III) (hydr)oxide Minerals in the Presence of Diverse Ligands and over a Broad pH Range

Janet Gordon Hering

Dissolution of Fe(III) (hydr)oxide minerals by siderophores (i.e., Fe-specific, biogenic ligands) is an important step in Fe acquisition in environments where Fe availability is low. The observed coexudation of reductants and ligands has raised the questio ...

AMER CHEMICAL SOC2019

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