TML&TDL-BP/RI-Score/GOLD/AUTODOCK-VINA
Schrodinger, GOLD, AUTODOCK VINA, R-TDA, Javaplex, Scikit-learn
PHE211 and PHE70 are set as flexible in docking.
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.
No
Close_Dock/Autodock Vina/Schrodinger
Autodock Vina/Schrodinger
(prepwizard) -propka_pH 7.0
(prepwizard) -fillsidechains -s # fillsidechains for target protein
(ligprep) -adjust_itc -ph
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.
size_x = 15
size_y = 15
size_z = 15
exhaustiveness = 50
num_modes = 1000
energy_range = 10
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.
No
Yes