Sampling molecular conformations and dynamics in a multiuser virtual reality framework

M O'Connor, HM Deeks, E Dawn, O Metatla… - Science …, 2018 - science.org
We describe a framework for interactive molecular dynamics in a multiuser virtual reality (VR)
environment, combining rigorous cloud-mounted atomistic physics simulations with …

[HTML][HTML] Discovery of SARS-CoV-2 M pro peptide inhibitors from modelling substrate and ligand binding

…, TR Malla, RM Twidale, T John, HM Deeks… - Chemical …, 2021 - pubs.rsc.org
The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising
drug target, but little is known about structural aspects of how it binds to its 11 natural cleavage …

[HTML][HTML] Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

MB O'Connor, SJ Bennie, HM Deeks… - The Journal of …, 2019 - pubs.aip.org
As molecular scientists have made progress in their ability to engineer nanoscale molecular
structure, we face new challenges in our ability to engineer molecular dynamics (MD) and …

Interactive molecular dynamics in virtual reality is an effective tool for flexible substrate and inhibitor docking to the SARS-CoV-2 main protease

HM Deeks, RK Walters, J Barnoud… - Journal of chemical …, 2020 - ACS Publications
The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts
for COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) …

[HTML][HTML] Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking

HM Deeks, RK Walters, SR Hare, MB O'Connor… - Plos one, 2020 - journals.plos.org
Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that
separate bound and unbound states require extensive sampling that consumes significant …

[HTML][HTML] Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists

RJ Shannon, HM Deeks, E Burfoot, E Clark… - The Journal of …, 2021 - pubs.aip.org
The emerging fields of citizen science and gamification reformulate scientific problems as
games or puzzles to be solved. Through engaging the wider non-scientific community, …

[HTML][HTML] Free energy along drug-protein binding pathways interactively sampled in virtual reality

HM Deeks, K Zinovjev, J Barnoud, AJ Mulholland… - Scientific Reports, 2023 - nature.com
We describe a two-step approach for combining interactive molecular dynamics in virtual
reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological …

Somatic practices for understanding real, imagined, and virtual realities

LM Thomas, HM Deeks, AJ Jones, O Metatla… - arXiv preprint arXiv …, 2019 - arxiv.org
In most VR experiences, the visual sense dominates other modes of sensory input, encouraging
non-visual senses to respond as if the visual were real. The simulated visual world thus …

[PDF][PDF] Biomolecular Applications of Interactive Molecular Dynamics in Virtual Reality

HM Deeks - 2021 - research-information.bris.ac.uk
Deeks, know me better than anyone else and have supported me unconditionally throughout
this time. My mother, Mary Deeks, … my late father, Henry Deeks, who I am deeply saddened …

Discovery of SARS-CoV-2 Mpro Peptide Inhibitors from Modelling Substrate and Ligand Binding (preprint)

…, RK Walters, TR Malla, RM Twidale, T John, HM Deeks… - 2021 - pesquisa.bvsalud.org
The main protease (Mpro) of SARS-CoV-2 is central to its viral lifecycle and is a promising
drug target, but little is known concerning structural aspects of how it binds to its 11 natural …