Bouyssié D, Lesne J, Locard-Paulet M, Albigot R, Burlet-Schiltz O, Marcoux J. HDX-Viewer: interactive 3D visualization of hydrogen-deuterium exchange data.
Bioinformatics 2020;
35:5331-5333. [PMID:
31287496 PMCID:
PMC6954641 DOI:
10.1093/bioinformatics/btz550]
[Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 11/26/2022] Open
Abstract
Summary
With the advent of fully automated sample preparation robots for Hydrogen–Deuterium eXchange coupled to Mass Spectrometry (HDX-MS), this method has become paramount for ligand binding or epitope mapping screening, both in academic research and biopharmaceutical industries. However, bridging the gap between commercial HDX-MS software (for raw data interpretation) and molecular viewers (to map experiment results onto a 3D structure for biological interpretation) remains laborious and requires simple but sometimes limiting coding skills. We solved this bottleneck by developing HDX-Viewer, an open-source web-based application that facilitates and quickens HDX-MS data analysis. This user-friendly application automatically incorporates HDX-MS data from a custom template or commercial HDX-MS software in PDB files, and uploads them to an online 3D molecular viewer, thereby facilitating their visualization and biological interpretation.
Availability and implementation
The HDX-Viewer web application is released under the CeCILL (http://www.cecill.info) and GNU LGPL licenses and can be found at https://masstools.ipbs.fr/hdx-viewer. The source code is available at https://github.com/david-bouyssie/hdx-viewer.
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