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Homology Modeling and Binding Site Analysis of SARS-CoV-2 (COVID-19) Main Protease 3D Structure
Abstract
The severe acute respiratory syndrome coronavirus 2 (SAR-Cov-2) caused the coronavirus (COVID-19) pandemic. The global concern is the discovery of a new target drug for the total cure. Recently, some research showed that a few COVID-19 enzymes may have been contemplated to be potential drug targets, but not much is known about its structural biology. This research investigates the 3-D structure of protease SAR-CoV-2. The tertiary structure was determined by homology modeling. The Swiss-Model workspace and the basic local alignment search tool (BLAST) were employed for modeling, and the resulted model was validated with programs that include PROCHECK, Verify3D, and QMEAN to ascertain reliability. To establish the structures that fitted, HHBlits software was employed. To verify the structure quality, a Ramachandran plot was exploited. The binding site was determined using CASTp and DeepSite algorithms, which showed that this protein can be exploited as a prospective pharmaceutical target. Albeit further experimentation is required as a COVID-19 virus vaccine-design/target-drug.
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