Desenvolvimento de uma plataforma web para análise de Ligações de Hidrogênio em sistemas proteína-água

Abstract

Hydrogen Bonds (HBs) are attractive interactions usually established between a dipole formed by a highly electronegative atom (X) and a Hydrogen (X--H), with another electronegative atom (X—H .... Y). The HBs are very important in the formation of the secondary and tertiary structures of proteins and are responsible for many of the characteristics of water that makes life possible. Due to the importance of HBs, several studies have been done with the intention of understanding the principles that govern their formation, as well as their influence on the structure of biomolecules. One of the main biases for the study of LHs is the computational approach, through the use of Molecular Dynamics tools, such as the GROMACS package, which allows the identification of LHs, but not their energy. In this way, the tool g_ener_hb was developed, presenting the ability to identify and measure the energies of the LHs formed in systems derived from simulation made by GROMACS. However, due to the fact that its installation and configuration can be challenging for people with no experience in Linux operating systems, this work was executed in order to facilitate the study of LHs by producing an online platform based on the g_ener_hb and GROMACS tools analysis process , capable of analyzing the energy of the LHs, in a simple and effective way. The platform was developed using Python as the main programming language, along with the Django framework, for organizing and optimizing web development. The SQLite3 database manager was used to store the parameters of processing and user data. HTML, CSS and JavaScript were used in the development of the interface. The JS JQuery and NGL libraries were used for interaction with the server, and for visualizing proteins, respectively. Finally, the platform was installed and configured on a server with the Ubuntu Server 16.04 operating system, using the Gunicorn, Nginx and Supervisor tools, in order to allow users access. The platform presented coherent operation, allowing the user to choose the parameters in intuitive screens, executing the processing and returning the resulting files.