Computational protocol: 2-(3, 4-dihydroxybenzylidene)malononitrile as a novel anti-melanogenic compound

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Protocol publication

[…] Dedicator of cytokinesis 6 (Dock6) was used for the in silico protein–ligand docking simulation. The results from Dock6 were confirmed using the AutoDock4.2 program. The 3D structure of tyrosinase was used in the crystal structure of Agaricus bisporus (PDB ID: 2Y9X). The predefined binding site of tyrosine was used as a docking pocket. The following steps were performed to prepare the structures of compounds for docking simulation, (1) 2D structures were converted into 3D structures, (2) charges were calculated, and (3) hydrogen atoms were added using the ChemOffice program (http://www.cambridgesoft.com). Afterwards, docking simulations between tyrosinase and BMN11 or kojic acid were performed. The predicted hydrogen bonding residues between different compounds and tyrosinase, and generation of pharmacophores were investigated with the LigandScout 3.0 software. […]

Pipeline specifications

Software tools AutoDock, LigandScout
Application Protein interaction analysis
Chemicals Hydrogen