Glide module

Next, the receptor grid generation platform of Schrodinger's Glide module was used to generate a grid of size 20 × 20 × 20 Å around the literature reported binding pocket.^{38 (link)} Molecular docking of polydatin with the above-described grids was performed using the Glide module of Schrodinger.

A docking grid was generated for each HLA class II protein by using the receptor grid generation option of the glide module of Schrödinger suite. The receptor grid box was prepared by keeping the centroid of the resident peptide as the center of the box. The size of the box was set at the minimum that can accommodate a ligand similar in size to the resident peptide. The resident peptides were excluded from the grid. All the prepared peptides were then docked to each of the HLA class II alleles in a three-step process by using the ligand docking option of the glide module of Schrödinger suite. Initially, a High-Throughput Virtual Screening (HTVS) was performed with all the peptides against each HLA-II allele. The peptide poses for each HLA class II allele with glide scores better than –10 kcal/mol were used for standard precision (SP) docking to that allele. The peptide poses that docked with glide scores better than –10 kcal/mol were then docked using the extra precision (XP) module to the corresponding allele.