tn7sk-LigandScoringProtocol.txt

Name

RI-Score-K1/TDL-BP/AutoDock Vina

Software

RI-Score/TDL-BP/AutoDock Vina

Parameters

Use RI-Score and TDL-BP with default parameters
Use RandomForest package in R with number of trees = 550 and total number of features

Method

Use RI-Score, TDL-BP and AutoDock Vina to predict binding energies

Answer 1

No

tn7sk-PosePredictionProtocol.txt

Name

Constraint_IFD/Schrodinger

Software

Schrodinger

System Preparation Parameters

(prepwizard) -propka_pH 7.0
(prepwizard) -fillsidechains -s # fillsidechains for target protein
(ligprep) -adjust_itc -ph

System Preparation Method

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.

Pose Prediction Parameters

Use default parameters in Induced Fit Docking
Restrict docking to ligand's position binded to wild type with a tolerance of 3.0 \AA

Pose Prediction Method

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.

Answer 1

No

Answer 2

Yes