Computational protocol: Mechanistic insight to ROS and Apoptosis regulated cytotoxicity inferred by Green synthesized CuO nanoparticles from Calotropis gigantea to Embryonic Zebrafish

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Protocol publication

[…] Molecular docking analysis was done by using Autodock 4.2 with CuO as ligand and he1a, sod1, tp53 as receptor proteins. Chimera was used for drawing the structure of CuO and its geometry was optimized using Gaussian 03 program. Energy minimization was carried out using Chimera program for the receptor proteins. The parameters for CuO have been set for Autodock 4.2. Grid dimensions were set to 40 × 40 × 40, with a spacing of 1 Å for all the protein receptors. Lamarckian genetic algorithms (LGA) were used for grid dimensions. The population size of 150 with a maximum number of evaluations set to 2500000 and maximal generations were used with the help of Genetic algorithm for docking runs. The post-docking analysis was performed using conformational clustering’s visualized by Chimera and Discovery Studio Visualizer. 2D interaction plots have been derived from the receptor complexes having TiO2 as a ligand by using LigPlot+. […]

Pipeline specifications

Software tools AutoDock, Discovery Studio® Visualizer, LigPlot+
Application Protein interaction analysis
Organisms Danio rerio, Homo sapiens
Diseases Drug-Related Side Effects and Adverse Reactions
Chemicals Amino Acids, Hydrogen