2.10. Vaccine Candidate Molecular Docking with an Immune Receptor (TLR-4)

For molecular docking of the vaccine candidate, the crystal structure of TLR-4 (PDB ID: 4G8A) was obtained from the PDB (Protein Data Bank) database (https://www.rcsb.org (accessed on 5 April 2023). Protein was prepared before docking by removing water molecules and each crystallized ligand with PyMOL (https://www.charmm.org/ (accessed on 7 April 2023). Additionally, energy minimization was performed on the structure. The vaccine candidate was docked using the HDOCK server (http://hdock.phys.hust.edu.cn/ (accessed on 9 April 2023) [38] using default server parameters. The PyMOL tool (http://pymol.org (accessed on 25 April 2023) was used to visualize and analyze docked complexes.