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
Free_IFD/Schrodinger
Schrodinger
(prepwizard) -propka_pH 7.0
(prepwizard) -fillsidechains -s # fillsidechains for target protein
(ligprep) -adjust_itc -ph
Use Homology Modeling in Maestro to build protein structure from given sequence. 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. The mutant structures was obtained by using 'Mutate Residues' module in Maestro.
Use default parameters in Induced Fit Docking
For the wild type, ligand pose was obtained by aligning to the most similar ligands selected from Protein Data Bank. For the mutant structures, Induced Fit Docking was employed for the pose generations.
No
Yes