3D structural prediction, analysis and validation of Sars-Cov-2 protein molecules

Abstract

Knowing the structure of a protein is of enormous importance but presents great theoretical and technological challenges. The COVID-19 pandemic showed how important it was to be able to determine the structure and form of SARS-COV-2 to better understand its functioning and to be able to develop vaccines and combat drugs. This article presents mathematical-computational and physical-chemical aspects involved in the reconstruction and validation of the three-dimensional molecular conformations of SARS-CoV-2 virus proteins, including the variant discovered in patients from Brazil  in 2021, the lineage B.1.1.28/P.1. The methodology used is based on the sequencing of the virus protein through the incorporation of new in silico mutations in already known structures, the result is then submitted to computational reconstruction using an enumerative feasibility algorithm validated by the Ramachandran diagram and alignment structural. After the structural reconstruction of the virus, a stability study is performed with the protein generated through classical molecular dynamics.