3.4 Hydrogen bonding analysis
Hydrogen bonding between a ligand and receptor stabilizes their interaction [16]. It also shows the specificity, metabolization, and adsorption of the drug. To further explain the conformational stability, the total number of hydrogen bonds between each scaffold-receptor was analyzed (Fig.4). It indicated that the scFv and EGFR DIII complex shows strong bonding interaction throughout the 50 ns of MD simulations. Analyzing the reference complex of scFv with the receptor, around 13 hydrogen bonds (Orange) were observed in the complex. At the same time, 13, 5, and 4 residues in Scaf1 (Gray), Scaf2 (Blue), and Scaf3 (Red) were involved in hydrogen interaction with the receptor. The above detailed H-bond analysis showed that Scaf1 was bound to the EGFR DIII as effectively and tightly as the reference molecule scFv.