Computational protocol: Phytochemicals Mediate the Expression and Activity of OCTN2 as Activators of the PPARγ/RXRα Pathway

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Protocol publication

[…] To investigate the possible binding sites of phytochemicals in PPARγ protein, the molecular docking analysis was conducted by Autodock Tools (ADTs) v1.1 and the Autodock v4.0.5 program, including Autogrid and Autodock software (Copyright_1991e2000, the Scripps Research Institute). The co-crystalized structure of PPARγ (PBD ID: 2PRG) was obtained from the RCSB Protein Data Bank (PBD), and 3D structures of the three phytochemicals were downloaded from the PubChem website. The rigid roots of each phytochemical were defined automatically, and the amide bonds were made non-rotatable by ADT. The active site of PPARγ was considered a rigid molecule, whereas the phytochemicals were treated as being flexible. The internal default parameters in the AutoDock software were used to analyze all of the variables, except for the number of docking runs (10), the medium number of energy evaluations on genetic algorithm eGA (2, 500,000) and the maximum number of generations in GA (5000). Following the completion of the docking search, the final compound pose was located by evaluating AutoDock’s empirical scoring function in which the conformation with the lowest docked energy value was chosen as the best. The docking model and hydrogen bonds were predicted by ADT and Pymol software (DeLano Scientific LLC). […]

Pipeline specifications

Software tools AutoDock, PyMOL
Application Protein interaction analysis
Diseases Colorectal Neoplasms
Chemicals Amino Acids, Curcumin, Hydrogen