Computational protocol: Investigation of Inclusion Complex of Patchouli Alcohol with β-Cyclodextrin

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Protocol publication

[…] In order to investigate and confirm the inclusion behavior of guest patchouli alcohol (PA) into host (β-CD), autodock 4.2.3 was used to simulate the supermolecular structure of the inclusion complex with regular genetic algorithm method [].The docked conformation which had the least binding energy was selected to analyze the mode of binding. The interaction of host-guest were developed by PyMol molecular viewer [].Amber 11 Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) program was used to calculate the binding delta Gibbs free energy. The docking result was also optimized by molecular simulation using amber 11 program []. The optimization ran for 2 ns. The binding energy (ΔbGo) was calculated according to : ΔbGo=Ecomplex−Ehost−Eguest(1)The calculated energy of PA, β-CD and the inclusion complex molecules were Ehost, Eguest, and Ecomplex (kcal/mol), respectively. […]

Pipeline specifications

Software tools AutoDock, PyMOL, AMBER
Application Protein interaction analysis
Organisms Dipturus trachyderma