Structural biology in the clouds: The WeNMR-EOSC Ecosystem

no code implementations • 2 Jul 2021 • Rodrigo Vargas Honorato, Panagiotis I. Koukos, Brian Jiménez-García, Andrei Tsaregorodtsev, Marco Verlato, Andrea Giachetti, Antonio Rosato, Alexandre M. J. J. Bonvin

Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details.

Distributed Computing

Information-Driven Modeling of Biomolecular Complexes

no code implementations • 12 Mar 2021 • 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.

Molecular Docking

Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry

no code implementations • 1 Jul 2020 • Alexander Leitner, Alexandre M. J. J. Bonvin, Christoph H. Borchers, Robert J. Chalkley, Julia Chamot-Rooke, Colin W. Combe, Jürgen Cox, Meng-Qiu Dong, Lutz Fischer, Michael Götze, Fabio C. Gozzo, Albert J. R. Heck, Michael R. Hoopmann, Lan Huang, Yasushi Ishihama, Andrew R. Jones, Nir Kalisman, Oliver Kohlbacher, Karl Mechtler, Robert L. Moritz, Eugen Netz, Petr Novak, Evgeniy Petrotchenko, Andrej Sali, Richard A. Scheltema, Carla Schmidt, David Schriemer, Andrea Sinz, Frank Sobott, Florian Stengel, Konstantinos Thalassinos, Henning Urlaub, Rosa Viner, Juan A. Vizcaino, Marc R. Wilkins, Juri Rappsilber

Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination, conformation analysis and mapping protein interactions in complex mixtures.

MENSADB: A Thorough Structural Analysis of Membrane Protein Dimers

1 code implementation • 6 Feb 2019 • Pedro Matos-Filipe, António J. Preto, Panagiotis I. Koukos, Joana Mourão, Alexandre M. J. J. Bonvin, Irina S. Moreira

Membrane Proteins (MPs) account for around 15-39% of the human proteome and assume a critical role in a vast set of cellular and physiological mechanisms, including molecular transport, nutrient uptake, toxin and waste product clearance, respiration, and signaling.