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
Align_close/AutoDock Vina/Schrodinger
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.
Solvation model = VSGB
Force field = OPLS3
Refine atoms within 10.0 \AA of ligand
Sampling algorithm = Local optimization
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.
No
Yes