The NMR structure of a mutated c-MYC G-quadruplex (PDB 2MGN) was used to perform docking study on ligands 2 and 3 . The three-dimensional structure of small molecules was sketched with DS viewer 3.5. Autodock Tools (version 1.5.6) was used for converting structure files to pdbqt format (49 (link)). The docking study was carried out by using AutoDock Vina program (50 (link)). The dimensions of the active site box were chosen to be large enough to encompass the entire G4 structures. An exhaustiveness of 100 was used and other parameters were left as default.
Protocol detail
Computational Docking of c-MYC G4 Ligands
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G quadruplex
Ligands
Corresponding Organization : Wuyi University
Other organizations : Thunder Bay Regional Research Institute, Lakehead University, Sun Yat-sen University
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Variable analysis
independent variables
- Ligands 2 and 3
- Docking study results
- NMR structure of a mutated c-MYC G-quadruplex (PDB 2MGN)
- Dimensions of the active site box
- Exhaustiveness of 100
- Other parameters left as default
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