Interactive flexible-receptor molecular docking in VR using DockIT

Research output: Contribution to journalArticlepeer-review

Abstract

Interactive docking enables the user to guide and control the docking of two biomolecules into a binding pose. It is of particular use when the binding site is known and is thought to be applicable to structure-based drug design (SBDD) and educating students about biomolecular interactions. For SBDD, it enables expertise and intuition to be brought to bear in the drug design process. In education, it can teach students about the most basic level of biomolecular function. Here, we introduce DockIT for virtual reality (VR) that uses a VR headset and hand-held controllers. Using the method of linear response on explicit solvent molecular dynamics simulations, DockIT can model both global and local conformational changes within the receptor due to forces of interaction with the ligand. It has real-time flexible molecular surface rendering and can show the real-time formation and breaking of hydrogen bonds, both between the ligand and receptor and within the receptor itself as it smoothly changes conformation.

Original languageEnglish
JournalJournal of Chemical Information and Modeling
Early online date18 Nov 2022
DOIs
Publication statusE-pub ahead of print - 18 Nov 2022

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