Touching proteins with virtual bare hands: how to visualize protein-drug complexes and their dynamics in virtual reality

TL;DR

This paper introduces a free virtual reality software pipeline for detailed 3D visualization of protein-drug complexes, combined with fast algorithms to simulate protein flexibility, enhancing drug design insights.

Contribution

It presents a novel VR visualization tool for protein structures integrated with dynamic simulation algorithms, improving structural analysis for drug discovery.

Findings

VR visualization offers more precise atomic interaction insights.

The pipeline is freely available and compatible with affordable hardware.

Simulating protein flexibility reveals hidden molecular interactions.

Abstract

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more precise visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). In this work, we present a freely available software pipeline for visualising protein structures through VR. New customer hardware, such as the HTC Vive and the Oculus Rift utilized in this study, are available at reasonable prices. Moreover, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-lead drug design by exposing molecular interactions that might be hidden in the less informative static models.