Scoring using AutoDock Vina
CDOCKER1.0 (CHARMM), ParamChem 1.0.0 and AutoDock Vina
Assuming pH 7 to assign the ligand's protanation state.
Simulated annealing is used to find 200 initial conformations of each ligand. Each conformation is docked onto crystal structure of protein 3OKI and 3DCT with CDOCKER. The protein structures are fixed rigid. The 5 lowest energy poses (with rmsd > 1.0 Angstrom) of each ligand for each protein structure were selected. These 10 poses were rescored with AutoDock Vina and the 5 lowest estimated free energy poses were submitted as pose predictions. The lowest free energy was used to rank the ligand.
Docking using CDOCKER from CHARMM plus Scoring using AutoDock Vina
CDOCKER1.0 (CHARMM), ParamChem 1.0.0 and AutoDock Vina
Assuming pH 7 to assign the ligand's protanation state.
ForceField: CHARMM36 and CHARMM General Force Field (CGenff3.0.1)
The ligands are assigned protanation states assuming pH of 7.0 and are parameterized with CGenff force field.
The parameters in the CDOCKER paper DOI:10.1002/jcc.10306 (Table 1) were used.
Simulated annealing is used to find 200 initial conformations of each ligand. Each conformation is docked onto crystal structure of protein 3OKI and 3DCT with CDOCKER. The protein structures are fixed rigid. The 5 lowest energy poses (with rmsd > 1.0 Angstrom) of each ligand for each protein structure were selected. These 10 poses were rescored with AutoDock Vina and the 5 lowest estimated free energy poses were submitted.