Name

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

Software

PQB2PQR, Javaplex, R-TDA, Scikit-learn

Parameters

NA

Method

Machine learning based method using the selected top poses.

Answer 1

No

Name

Close_Dock/Autodock Vina/Schrodinger

Software

Autodock Vina/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. Binding site is determined by using the ligand's position in the reference protein ultilized in structure prediction procedure.

Pose Prediction Parameters

size_x = 15
size_y = 15
size_z = 15
exhaustiveness = 50
num_modes = 1000
energy_range = 10

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. Use Autodock Vina to dock the target ligand to that receptor. The top pose was selected based on the Autodock Vina's energy.

Answer 1

No

Answer 2

Yes