Computational protocol: A small molecule, (E)-2-methoxy-4-(3-(4-methoxyphenyl) prop-1-en-1-yl) phenol suppresses tumor growth via inhibition of IkappaB kinase β in colorectal cancer in vivo and in vitro

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[…] Docking studies between IKKβ and MMPP was performed using Autodock VINA []. IKKβ crystal structure was used in the docking experiments and conditioned using AutodockTools by adding all polar hydrogen atoms. Three dimensional structures of IKKβ-DNA complexes were retrieved from the Protein Data Bank (PDB codes: 3BRT). Starting from the co-crystallized complexes, the IKKβ monomer chain (IKKβ from 3BRT), MMPP for docking were prepared using Maestro graphical interface. The grid box was centered on the IKKβ monomer and the size of the grid box was adjusted to include the whole monomer. Docking experiments were performed at various exhaustiveness values of the defaults: 16, 24, 32, 40 and 60. Molecular graphics for the best binding model was generated using Discovery Studio Visualizer 2.0. […]

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