PMC:7245302 / 12205-13173 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/7245302","sourcedb":"PMC","sourceid":"7245302","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7245302","text":"2.6 MEPVC Docking and Refinement\nThe technique of molecular docking was utilized to predict conformation of the MEPVC with respect to a suitable innate immune receptor. This analysis plays a significant role to determine the high-affinity contacts amid the vaccine construct and the immune receptor. The PDB ID: 4G8A and TLR3 PDB ID: 2A0Z were retrieved from the Protein Data Bank (PDB) for the TLR4 and TLR3, respectively. Blind docking employed to calculate the regular pose of the vaccine construct with the mentioned receptors using an online PATCHDOCK server [42]. The resulting structures were further refined using the Fast Interaction Refinement in Molecular Docking (FireDock) [43]. The top ranked complex with the minimum global energy was selected and used to analyse the binding pose and intermolecular connections using UCSF Chimera 1.13.1 [44], Discovery Studio (DS) Visualizer 17.2.0 [45].16349, and Visual Molecular Dynamics (VMD) 1.9.3 software 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