DockIT: a tool for interactive molecular docking and molecular complex construction

Abstract

Abstract Summary 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 relative position and orientation, either with a mouse and keyboard, or with a haptic device. 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. Availability and implementation DockIT is available free of charge for non-commercial use at http://www.haptimol.co.uk/downloads.htm. It requires a windows computer with GPU that supports OpenCL 1.2 and OpenGL 4.0. It may be used with a mouse and keyboard, or a haptic device from 3DSystems.