PMC:7441777 / 12501-13255 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7441777","sourcedb":"PMC","sourceid":"7441777","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7441777","text":"2.1.3. Docking studies using AutoDock Vina\nThe energy-minimized structure of all the natural polyphenols, remdesivir, and GTP were docked with the receptor (RdRp of SARS-CoV-2) using AutoDock Vina 1.1.2 (Trott \u0026 Olson, 2010). The ligand files were further saved in PDBQT file format, a modified PDB format containing atomic charges, atom type definitions for ligands, and topological information (rotatable bonds). A grid box (30 Å × 30 Å × 30 Å) centered at (121, 120, 125) Å for the SARS-CoV-2 RdRp, was used in the docking experiments. After the receptor-ligand preparation, docking runs were started from the command prompt. The lowest binding energy and best-docked conformation were considered as the ligand molecule with maximum binding 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