Computational protocol: C-Kit Binding Properties of Hesperidin (a Major Component of KMP6) as a Potential Anti-Allergic Agent

Similar protocols

Protocol publication

[…] Computer-aided docking simulation was performed by Surflex-Dock (Tripos, St. Louis, MO). The molecular model for the receptor protein, c-kit was obtained from the Protein Data Bank (PDB id 2E9W) with further energy-minimization. The 3D coordinates of each component were prepared by a molecular sketch module. All molecular modeling work was conducted using by a SYBYL X 1.1 package. To obtain an accurate binding mode and affinity data, docking was conducted in the Geom mode of Surfelx-Dock. A 6 Å of an expanded search grid, a maximum of 20 conformations per fragment, and a maximum of 100 rotatable bonds per molecule were used as general docking parameters. Spin alignment was activated with a search density of 3 Å and 12 spins per alignment. The docked pose for each component with c-kit was ranked according to Surflex-Dock Score. […]

Pipeline specifications

Software tools Surflex-Dock, Sybyl-X
Application Protein interaction analysis
Organisms Rattus norvegicus
Diseases Carcinoma, Renal Cell, Hypersensitivity
Chemicals Hesperidin