Excited to report on work we’ve just posted to the arXiv, describing interactive molecular dynamics in virtual reality (iMD-VR) using the open-source Narupa framework as an efficient strategy for generating reversible protein-ligand binding and unbinding pathways.
The paper outlines an experimental protocol which enables both expert and novice 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. It’s been an open question whether iMD-VR tools afford sufficient control for users to carry out detailed molecular manipulations in complex systems like biomolecules. I’m excited because these results indicate that it is possible to generate reversible binding pathways that recover crystallographic poses, offering a new approach for generating protein/ligand binding hypotheses.
Supplementary files are available here.