ArticlePloS one2020
Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Elements and roadmap for interactive molecular graphics and modeling "in the Holodeck".Protein science : a publication of the Protein Society · 2026Article
- Molecular Studies and Advanced Visualization of the Trapping of Methane Nanobubbles during Hydrate Growth.The journal of physical chemistry. B · 2025Article
- Interactive molecular dynamics in virtual reality for modelling materials and catalysts.Journal of molecular graphics & modelling · 2023Article
- Free energy along drug-protein binding pathways interactively sampled in virtual reality.Scientific reports · 2023Article
- Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots.Journal of integrative bioinformatics · 2023Article
- W254 in furin functions as a molecular gate promoting anti-viral drug binding: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics.Computational and structural biotechnology journal · 2023Article
- Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery.Molecules (Basel, Switzerland) · 2022Review
- Group VR experiences can produce ego attenuation and connectedness comparable to psychedelics.Scientific reports · 2022Article
- UDock2: interactive real-time multi-body protein-protein docking software.Bioinformatics (Oxford, England) · 2022Article
- Discovery of SARS-CoV-2 MChemical science · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
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 computational resources. Here, we describe the use of interactive molecular dynamics in virtual reality (iMD-VR) as an accurate low-cost strategy for flexible protein-ligand docking. We outline an experimental protocol which enables expert iMD-VR users to guide ligands into and out of the binding pockets of trypsin, neuraminidase, and HIV-1 protease, and recreate their respective crystallographic protein-ligand binding poses within 5-10 minutes. Following a brief training phase, our studies shown that iMD-VR novices were able to generate unbinding and rebinding pathways on similar timescales as iMD-VR experts, with the majority able to recover binding poses within 2.15 Å RMSD of the crystallographic binding pose. These results indicate that iMD-VR affords sufficient control for users to carry out the detailed atomic manipulations required to dock flexible ligands into dynamic enzyme active sites and recover crystallographic poses, offering an interesting new approach for simulating drug docking and generating binding hypotheses.
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Registered trials
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