The 13
studied compounds and CP were docked to structures of DNA gyrase (PDB
ID:5BTC )48 (link) and DNA topoisomerase IV (PDB ID: 3RAD )49 (link) (see Table S2 ). The docking
procedure is as follows. Ligand structures were generated using the
Automated Topology Builder (ATB version 2.2),56 (link) and topologies were created using the Avogadro57 (link) program. Docking calculations and data analysis were performed
using AutoDock4 (v. 4.2) and AutoDockTools4 programs, respectively.58 (link) 1000 models were generated for each complex
during the docking procedure. Preferred binding modes were selected
based on structural clustering with an rmsd cut-off value of 3 Å.
The central structure of the largest cluster was selected as the final
ligand-docked structure for each complex.
studied compounds and CP were docked to structures of DNA gyrase (PDB
ID:
procedure is as follows. Ligand structures were generated using the
Automated Topology Builder (ATB version 2.2),56 (link) and topologies were created using the Avogadro57 (link) program. Docking calculations and data analysis were performed
using AutoDock4 (v. 4.2) and AutoDockTools4 programs, respectively.58 (link) 1000 models were generated for each complex
during the docking procedure. Preferred binding modes were selected
based on structural clustering with an rmsd cut-off value of 3 Å.
The central structure of the largest cluster was selected as the final
ligand-docked structure for each complex.
Free full text: Click here
