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HaptiMOL DockIT
DockIT is a tool that has a unique set of physical and graphical features for interactive molecular docking. It enables the user to bring a ligand and a receptor into a docking pose by controlling the ligand position, either with a mouse and keyboard, a haptic device or VR touch controllers. The Oculus Rift, RiftS or Meta Quest 2 (with link cable) are supported).
Receptor flexibility can also be incorporated. In order to model receptor flexibility we use the method of linear response for which we determine the variance-covariance matrix of atomic fluctuations from the trajectory of an explicit-solvent Molecular Dynamics simulation of the ligand-free receptor molecule. Atomic interactions are modelled using molecular dynamics-based force-fields with the force on the ligand being felt on a haptic device. Real-time calculation and display of intermolecular hydrogen bonds and multipoint collision detection either using maximum force or maximum atomic overlap, mean that together with the ability to monitor selected intermolecular atomic distances, the user can find physically feasible docking poses that satisfy distance constraints derived from experimental methods. With these features and the ability to output and reload docked structures it can be used to accurately build up large multi-component molecular systems in preparation for molecular dynamics simulation.
A movie of DockIT is available.
The following images are screenshots from the software.
An OpenCL enabled GPU is required to run the software.