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

Cross_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

Use Protein Data Bank to search for the proteins having the same macromolecule name as of the provided receptor. The target ligand was docked to these structures. The top pose was selected based on the Autodock Vina's energy.

Answer 1

No

Answer 2

Yes