RI-Score-K1/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
Constraint_IFD/Schrodinger
Schrodinger
(prepwizard) -propka_pH 7.0
(prepwizard) -fillsidechains -s # fillsidechains for target protein
(ligprep) -adjust_itc -ph
Use Homology Modeling in Maestro to build protein structure from given sequence. 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. The mutant structures was obtained by using 'Mutate Residues' module in Maestro.
Use default parameters in Induced Fit Docking
Restrict docking to ligand's position binded to wild type with a tolerance of 3.0 \AA
For the wild type, ligand pose was obtained by aligning to the most similar ligands selected from Protein Data Bank. For the mutant structures, Induced Fit Docking was employed for the pose generations.
No
Yes