yqoad-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

yqoad-PosePredictionProtocol.txt

Name

Align_target/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.

Pose Prediction Parameters

Solvation model = VSGB
Force field = OPLS3
Refine atoms within 10.0 \AA of ligand
Sampling algorithm = Local optimization

Pose Prediction Method

Each target ligand is aligned to its most similar structure available in Protein Data Bank. The algined ligand is optimized to the binding site of the receptor using Prime in Schrodinger.

Answer 1

No

Answer 2

Yes