| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T64 |
0-19 |
Sentence |
denotes |
Docking methodology |
| T65 |
20-142 |
Sentence |
denotes |
The flexible docking was performed using the refined spike protein of SARS-CoV (6CRV) and RBD domain of SARS-CoV-2 (6M0J). |
| T66 |
143-246 |
Sentence |
denotes |
The grid maps of the interaction energies of various atom types were pre-calculated using AutoGrid 4.2. |
| T67 |
247-447 |
Sentence |
denotes |
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. |
| T68 |
448-545 |
Sentence |
denotes |
The grid maps were centred on the corresponding ligand binding site within the protein structure. |
| T69 |
546-668 |
Sentence |
denotes |
Lamarckian Genetic Algorithm (LGA) was adopted to perform docking simulations using the following default parameters, viz. |
| T70 |
669-1026 |
Sentence |
denotes |
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. |
| T71 |
1027-1192 |
Sentence |
denotes |
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. |
| T72 |
1193-1348 |
Sentence |
denotes |
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. |
| T73 |
1349-1476 |
Sentence |
denotes |
The pose with the lowest ΔG-score was considered the best fitted one and was further analyzed for Ligand-receptor interactions. |
