Docking methodology
The flexible docking was performed using the refined spike protein of SARS-CoV (6CRV) and RBD domain of SARS-CoV-2 (6M0J). The grid maps of the interaction energies of various atom types were pre-calculated using AutoGrid 4.2. In each docking for spike surface glycoprotein and spike RBD, a grid box was created using a grid map of 45 × 45 × 45 points, 60 × 60 × 60 points with grid spacing of 0.375 Å and 0.420 Å respectively. The grid maps were centred on the corresponding ligand binding site within the protein structure.
Lamarckian Genetic Algorithm (LGA) was adopted to perform docking simulations using the following default parameters, viz. 100 independent runs with step sizes of 0.2 Å for translations and 5 Å for orientations and torsions, an initial population of random individuals with a population size of 150 individuals, a maximum of 2.5 × 106 energy evaluations, maximum number of generations of 27,000; mutation and crossover rates of 0.02 and 0.8 respectively and an elitism value of 1. All the computations were carried out on Cygwin and was used to generate both grid parameter file (.gpf file) and docking parameter file (.dpf file) for each ligand. The docked conformations of each ligand were ranked into clusters based on the binding energy and the top ranked conformations were used for further study. The pose with the lowest ΔG-score was considered the best fitted one and was further analyzed for Ligand-receptor interactions.