15 citations · 26 across the 5 of their papers we have counts for
7 papers · 1 filter
Ranking protein-protein models with large language models and graph neural networks
Xiaotong Xu, Alexandre M. J. J. Bonvin
Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural info…
Structural biology in the clouds: The WeNMR-EOSC Ecosystem
Rodrigo Vargas Honorato, Panagiotis I. Koukos, Brian Jiménez-García +5
Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of…
Information-Driven Modeling of Biomolecular Complexes
Charlotte W. van Noort, Rodrigo V. Honorato, Alexandre M. J. J. Bonvin
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very lar…
A protocol for information-driven antibody-antigen modelling with the HADDOCK2.4 webserver
Francesco Ambrosetti, Zuzana Jandova, Alexandre M. J. J. Bonvin
In the recent years, therapeutic use of antibodies has seen a huge growth, due to their inherent proprieties and technological advances in the methods used to study and characteriz…
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: Performance in pose prediction in the D3R-GC4
Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci +2
We report the performance of our newly introduced Ensemble Docking with Enhanced sampling of pocket Shape (EDES) protocol coupled to a template-based algorithm to generate near-nat…
Protein-protein modelling using cryo-EM restraints
Mikael Trellet, Gydo van Zundert, Alexandre M. J. J. Bonvin
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous…