Computational protocol: Tryptanthrin Inhibits Angiogenesis by Targeting the VEGFR2-Mediated ERK1/2 Signalling Pathway

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Protocol publication

[…] Interaction of tryptanthrin with the ATP-binding site in the kinase-insert domain-containing region (KDR) of VEGFR2 was measured by molecular docking analysis with AutoDock Vina v.1.0.2 . The crystal structure of VEGFR2 (PDB code 1YWN) was obtained from the Protein Data Bank. The docking parameters were set using default values with the grid box (size: 20 Å×20 Å×20 Å) encompassing the ATP-binding site . The binding modes of tryptanthrin with the lowest binding free energy to the ATP-binding site were chosen for subsequent confirmation of docking conformation. The simulation data were illustrated by PyMOL v.1.3 (Schrödinger, OR, USA) and Discovery Studio Visualizer (Accelrys, CA, USA). […]

Pipeline specifications

Software tools AutoDock Vina, PyMOL, Discovery Studio® Visualizer
Application Protein interaction analysis
Organisms Mus musculus, Homo sapiens
Diseases Neoplasms, Corneal Neovascularization
Chemicals Adenosine Triphosphate