Computational protocol: Echinacoside Increases Sperm Quantity in Rats by Targeting the Hypothalamic Androgen Receptor

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Protocol publication

[…] A molecular docking study was performed to investigate the binding mode of the compound ECH to human androgen receptor (AR) using Autodock vina 1.1.2 (http://vina.scripps.edu). The three-dimensional (3D) structure of AR (PDB ID: 2YHD) was downloaded from Protein Data Bank (http://www.rcsb.org/pdb/home/hone.do). The 3D structure of ECH was obtained by ChemBioDraw Ultra 14.0 and ChemBio 3D Ultra 14.0 software. The AutoDockTools 1.5.6 package (http://mgltools.scripps.edu) was employed to generate the docking input files. The search grid of AR was identified as center x: 36.141, center y: 8.513, and center z: 21.304 with dimensions size x: 15, size y: 15, and size z: 15. The value of exhaustiveness was set to 20. For Vina docking, the default parameters were used if it was not mentioned. The best-scoring pose as judged by the Vina docking score was chosen and visually analyzed using PyMOL 1.7.6 software (http://www.pymol.org). […]

Pipeline specifications

Software tools AutoDock Vina, AutoDock, PyMOL
Application Protein interaction analysis
Organisms Rattus norvegicus, Mus musculus
Diseases Infertility, Male, Nervous System Diseases
Chemicals Testosterone