Computational protocol: A Benzothiazole Derivative (5g) Induces DNA Damage And Potent G2/M Arrest In Cancer Cells

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Protocol publication

[…] Molecular docking studies were carried out using Autodock 4.2 program (PMID: 19399780). Briefly, 3D structure of CDK1 and CDK2 were retrieved from protein data bank (PDB ID: 5HQ0 and 2VTP, respectively). Ligand was removed and PDBQT files were generated for protein as well as 5g. Grid files were generated using the appropriate dimensions (5HQ0: 30.84, −69.63, 186.64 for X, Y and Z dimensions, respectively; 2VTP: 28.68, 5.31 and 60.28 for X, Y and Z dimensions, respectively). Rigid docking was carried out using Lamarckian genetic algorithm (GA run was kept 10 with medium search parameter). Best pose was selected according to lower binding energy and presented in the final image. Images were created with PyMOL (http://www.pymol.org/). […]

Pipeline specifications

Software tools AutoDock, PyMOL
Application Protein interaction analysis