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

• Published in: Scientific reports Vol. 13; no. 1; p. 16665
• Main Authors: Deeks, Helen M, Zinovjev, Kirill, Barnoud, Jonathan, Mulholland, Adrian J, van der Kamp, Marc W, Glowacki, David R
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 04.10.2023; Nature Publishing Group UK; Nature Portfolio
• Subjects: Benzamidine; Computer applications; Free energy; Humans; Ligands; Molecular Dynamics Simulation; Protein Binding; Proteins; Trypsin; Virtual Reality

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 processes at the molecular level. We refer to this combined approach as iMD-VR-FE. Stage one involves using a state-of-the-...