RI-Score-K1-V/TDL-BP/AutoDock Vina
RI-Score/TDL-BP/AutoDock Vina
Use RI-Score and TDL-BP with default parameters
Use RandomForest package in R with number of trees = 550 and total number of features
Use RI-Score, TDL-BP and AutoDock Vina to predict binding energies
No
Cross_Dock/Autodock Vina/Schrodinger
Autodock Vina/Schrodinger
(prepwizard) -propka_pH 7.0
(prepwizard) -fillsidechains -s # fillsidechains for target protein
(ligprep) -adjust_itc -ph
Maestro's prepwizard was used to optimize the protein with a standard pH value and fillsidechains option. Maestro's ligprep was used to generate optimized 3d structure of ligands from 2d structure. Binding site is determined by using the ligand's position in the reference protein ultilized in structure prediction procedure.
size_x = 15
size_y = 15
size_z = 15
exhaustiveness = 50
num_modes = 1000
energy_range = 10
Use Protein Data Bank to search for the proteins having the same macromolecule name as of the provided receptor. The target ligand was docked to these structures. The top pose was selected based on the Autodock Vina's energy.
No
Yes