SARS-CoV-2 papain-like protease molecular dynamics simulation


Molecular Dynamics Simulation is one of the most advantageous tools in the molecular biology and bioinformatics files, specifically in the drug design specification. MDS grants the researcher with the ability to model, simulate, and study a macromolecule or its interaction with a small molecule, in-silico. During the MDS process, energy and state equations are iteratively solved for an energy-minimized and equilibrated in terms of temperature and pressure, during a nano or micro second scale time frame, resulting in the trajectory of the atoms in the system, during the simulation. MDS brings insight into the realistic atomic behavior of the system. Herein, we have performed a molecular dynamics simulation for the Papain-Like protease of SARS-CoV-2, during a 10 ps time frame and in a 300K system. Papain-Like protease of COVID-19 agent could be the drug target for many drug-design studies and hence, MD simulation of this protein is of great importance to encounter the Coronavirus SARS-like diseases. The selected protein is accessible through the Protein Data Bank via the 6WZU accession number. Preprocessing and simulation steps are carried on using the Python environment and implementation of the GROMACS software in the bash environment, by utilizing an Nvidia K80/T4 Graphical Processing Unit (GPU). AMBER force filed is selected for the MDS process, energy-minimization, NVT, and NPT equilibriums for a 1 ps time frame are also ensured and resultant MD files in addition to trajectory files are submitted.

This project is carried on at Bioinformatics Camp (BioinfCamp), with the help of projects team, and under the supervision of Mr. Roohparvar. 


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