Development Of Protein Structure Visualization And Docking Programs In Virtual Reality

The main visualization tools of biological macromolecules can meet the needs of most researchers.However,these tools are difficult to bring new perspectives and ideas to the study of the structure and function of biological macromolecules due to the 2D display carrier and limited human-computer interaction methods.Virtual reality technology can make up for these shortcomings because of its immersion and interaction.In this work,we first developed a pipeline for visualization of molecular dynamics simulation trajectories and biomolecules structures in virtual reality,focusing on the photosynthesis system of purple bacteria.Interactively,users can "pick up" protein molecules and small pigment molecules for observation.It provides a new choice for the display of the structure research results of photosynthetic systems.Secondly,we got inspiration from multiplayer online protein folding games and developed a virtual reality-based protein docking game.Through this game,users can perform 3D spatial changes on protein receptors,and the spatial position of the original protein complex conformation is used as the game level judgment standard.This game platform can help users learn and understand the principle of protein docking.In addition,PDBTool,a plugin running in the virtual reality engine(Unreal Engine4),was developed to addressed the shortcomings of protein models losing biochemical information in virtual reality scenes.This plugin can directly read protein PDB files and construct a 3D model of the protein.Based on the PDBTool plugin,Doc Kit,a protein docking platform that uses molecular non-bond energy to evaluate the affinity of protein receptors and ligands,was developed.The molecular non-bond energy calculation is accelerated using CPU+GPU heterogeneous parallelism.When the protein docking platform is running,users can "grab" proteins and perform docking operations based on their 3D spatial perception and biochemical background knowledge,and obtain PDB files of the complex structure of the protein docking.We believe that virtual reality technology as a new computer simulation method can bring more value to the field of life science research.