Publication
3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme
Publications associées (36)
Microsecond Time-Resolved Cryo-Electron Microscopy
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 ...
EPFL2024New Methods for the Integrative Dynamic Modeling of Biomolecular Structures
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 ...
EPFL2021Fast 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 SOC2021SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions
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 ...
BMC2021Structure-Property Relationships in Complex Materials by Combining Supervised and Unsupervised Machine Learning
The work presented in this thesis combines supervised and unsupervised machine learning to examine structure-property relationships in databases of materials. While either supervised learning or unsupervised learning alone can be a powerful tool for assess ...
EPFL2021On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction
Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...
OXFORD UNIV PRESS2021Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction?
Matteo Dal Peraro, Luciano Andres Abriata
Protein dynamics is undoubtedly a pervasive ingredient in all biological functions. However, structural biology has been strongly driven by a static-centered view of protein architecture. We argue that the recent advances of cryo-electron microscopy (EM) h ...
AMER CHEMICAL SOC2020Protein Structural Information and Evolutionary Landscape by In Vitro Evolution
Protein structure is tightly intertwined with function according to the laws of evolution. Understanding how structure determines function has been the aim of structural biology for decades. Here, we have wondered instead whether it is possible to exploit ...
OXFORD UNIV PRESS2020rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics
Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Andreas Scheck, Jaume Bonet Martinez, Fabian Sesterhenn
BackgroundLarge-scale datasets of protein structures and sequences are becoming ubiquitous in many domains of biological research. Experimental approaches and computational modelling methods are generating biological data at an unprecedented rate. The deta ...
2019Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank
Michele Ceriotti, Piero Gasparotto, Benjamin Aaron Helfrecht, Federico Giberti
Rationalizing the structure and structure–property relations for complex materials such as polymers or biomolecules relies heavily on the identification of local atomic motifs, e.g., hydrogen bonds and secondary structure patterns, that are seen as buildin ...
2019