Name

TML&TDL-BP/RI-Score/GOLD/AUTODOCK-VINA

Software

Schrodinger, GOLD, AUTODOCK VINA, R-TDA, Javaplex, Scikit-learn

Parameters

PHE211 and PHE70 are set as flexible in docking.

Method

Ligands are prepared by Schrodinger. Docking is done by using GOLD. Poses are selected by plp and autodock vina scores. Binding free energy is predicted by topology based machine learning method.

Answer 1

No

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