Research And Implement Of Water-mediated Hydrogen Bond Calculation And Visualization

Hydrogen bond calculation provides an important foundation for exploring the molecular interaction mechanism in the studies of structure and function of biological macromolecules.Although many current software has the hydrogen bond calculation function based on the molecular simulation data,there are still the following limitations which include the lack of support for hydrogen bond(e.g.,water-mediated hydrogen bond)calculation,inadequate compatibility with input trajectory files and the absence of service for hydrogen bond visualization.Therefore,it is necessary to develop a more versatile and userfriendly software tool to achieve a more comprehensive analysis of interaction in the biomolecular systems.The main content of this paper is as follows:First,the implementation of water-mediated hydrogen bond calculation.In the support of direct hydrogen bond calculation and the third-party Python molecular dynamic analysis library,the classical geometric criterion of hydrogen bond is used to design and implement the water-mediated hydrogen bond calculation,which expands the capability of hydrogen bond calculation in biomolecules.And the program was compared with other hydrogen bond calculation program.Second,the visualization of hydrogen bond calculation results.Using the NGL Viewer biomolecular visualization Java Script library,the water-mediated hydrogen bond calculation results are presented in the form of a three-dimensional model.And the program was provided a web interface.Users can rotate,translate,zoom in and zoom out to observe the bonding situation,making it easier for users to understand the law of intermolecular interaction.To address the above issues,we remove excess water molecules by filtering,and use the cell list algorithm to accelerate the particle nearest neighbor search,implement the watermediated hydrogen bond calculation.This paper presents the design and implementation of water-mediated hydrogen bond calculation and visualization system based on Python,Java Script,Web GL technology and Django framework.The water-mediated hydrogen bond calculation and visualization integration software designed in this paper can support the calculation of various trajectory files and display the hydrogen bond calculation results through three-dimensional images.This software service is an extension and supplement of the commonly used hydrogen bond calculation program,and further provides theoretical support for the interaction study on the atomic level of biomolecules.