rdn3k-LigandScoringProtocol.txt

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

rdn3k-PosePredictionProtocol.txt

Name

Free_IFD/Schrodinger

Software

Schrodinger

System Preparation Parameters

(prepwizard) -propka_pH 7.0
(prepwizard) -fillsidechains -s # fillsidechains for target protein
(ligprep) -adjust_itc -ph

System Preparation Method

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.

Pose Prediction Parameters

Use default parameters in Induced Fit Docking

Pose Prediction Method

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.

Answer 1

No

Answer 2

Yes