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Abstract: The structural details and flexibilities of protein impose significant challenges to develop protein imprint, especially for the selection of functional monomer. Using NAMD, AutoDock 4 and AutoDock Vina, we investigated the formation of a high performance protein imprint on a nanosensor that detected human papillomavirus (HPV) biomarker protein E7 with high sensitivity. According to molecular dynamics, the phenolic oligomers were shown to assemble with the E7 protein and form a complex at specific targeting areas on the protein. Docking analysis efficiently screened chemical compounds by evaluating the binding affinity. A new parameter, i.e., average binding energy (Δ G/contact), was used together with binding energy (Δ G) to screen compounds. The screening went through 189 compounds and identified a subpopulation of 22 compounds showing unique characteristics of binding, and could potentially be used to develop the specific and robust imprint. Accordingly, the study implicated a novel approach to screen functional compounds for rational design of the protein imprint
Template and target information: protein, human papillomavirus (HPV) biomarker protein E7, E7
Author keywords: molecular imprint, rational design, Nanosensor, electropolymerization, biorecognition, Carbon nanotube, Docking, Molecular dynamics