vxc86-FreeEnergyProtocol.txt

Name

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

Software

RI-Score,TDL-BP,AutoDock Vina,Schrodinger

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

vxc86-PosePredictionProtocol.txt

Name

Align_close/AutoDock Vina/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

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.

Pose Prediction Parameters

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

Pose Prediction Method

The most similar ligand to a D3R ligand was selected from Protein Data Bank. The corresponding protein was used as a receptor of the target ligand. After aligning the interested ligand to its similar one, its structure was optimized to the binding site of the selected receptor using Prime in Schrodinger.

Answer 1

No

Answer 2

Yes