Hydrophobic Compounds Reshape Membrane Domains. - Jonathan Barnoud; Giulia Rossi; Siewert J. Marrink; Luca Monticelli (PLoS Comput. Biol., 2014)

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. - Richard J. Gowers; Max Linke; Jonathan Barnoud; Tyler J. E. Reddy; Manuel N. Melo; Sean L. Seyler; Jan J. Domanski; David L. Dotson; Sébastien Buchoux; Ian M. Kenney; Oliver Beckstein (SciPy, 2016)

Sharing Data from Molecular Simulations. - Mark James Abraham; Rossen Apostolov; Jonathan Barnoud; Paul Bauer; Christian Blau; Alexandre M. J. J. Bonvin; Matthieu Chavent; John D. Chodera; Karmen Condic-Jurkic; Lucie Delemotte; Helmut Grubmüller; Rebecca J. Howard; et al. (J. Chem. Inf. Model., 2019)

Narupa iMD: A VR-Enabled Multiplayer Framework for Streaming Interactive Molecular Simulations. - Alexander D. Jamieson-Binnie; Michael B. O'Connor; Jonathan Barnoud; Mark D. Wonnacott; Simon J. Bennie; David R. Glowacki (SIGGRAPH Immersive Pavilion, 2020)

Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease. - Helen M. Deeks; Rebecca Walters; Jonathan Barnoud; David R. Glowacki; Adrian J. Mulholland (J. Chem. Inf. Model., 2020)

Martinize2 and Vermouth: Unified Framework for Topology Generation. - Peter C. Kroon; Fabian Grünewald; Jonathan Barnoud; Marco van Tilburg; Paulo C. T. Souza; Tsjerk A. Wassenaar; Siewert-Jan Marrink (CoRR, 2022)

Measuring the Limit of Perception of Bond Stiffness of Interactive Molecules in VR via a Gamified Psychophysics Experiment. - Rhoslyn Roebuck Williams; Jonathan Barnoud; Luis Toledo; Till Holzapfel; David R. Glowacki (XR (1), 2024)

A Perspective on AI-Guided Molecular Simulations in VR: Exploring Strategies for Imitation Learning in Hyperdimensional Molecular Systems. - Mohamed Dhouioui; Jonathan Barnoud; Rhoslyn Roebuck Williams; Harry J. Stroud; Phil Bates; David R. Glowacki (CoRR, 2024)

NanoVer Server: A Python Package for Serving Real-Time Multi-User Interactive Molecular Dynamics in Virtual Reality. - Harry J. Stroud; Mark D. Wonnacott; Jonathan Barnoud; Rhoslyn Roebuck Williams; Mohamed Dhouioui; Adam McSloy; Ludovica Aisa; Luis E. Toledo; Phil Bates; Adrian J. Mulholland; David R. Glowacki (J. Open Source Softw., 2025)