Algorithmic Strategy for the Reconstruction and Validation of the Molecular Structure of SARS-CoV-2 Variants

• Clarice de Souza UFAM
• João Bessa UFAM
• Rosiane de Freitas UFAM
• Micael Oliveira UFAM
• Kelson Mota UFAM

DOI: https://doi.org/10.5753/bresci.2021.15790

Abstract

Mathematical-computational and physical-chemical aspects involved in the reconstruction of the three-dimensional molecular structure of SARS-CoV-2 proteins are addressed in this article, involving the P.1 variant detected in patients infected in Brazilian soil, especially those in the state of Amazonas. A study was carried out on the theoretical impact of P.1 through the structural reconstruction of proteins where mutagenesis was performed computationally and with the aid of the implementation of an implicit enumeration algorithm of feasibility, Branch-and-Prune, whose solutions were validated through the use of the Ramachandran chart. In this way, even with the absence of crystallographic structures characterizing these mutations, it was possible to computationally model a three-dimensional structure where, at the end, the structural alignment was performed with the crystallography of the ACE2-RBD complex

Keywords: algorithms, COVID-19 pandemic, distance geometry, SARS-CoV-2, structural reconstruction

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