Name

TML&TDL-BP/RI-Score/GOLD/AUTODOCK-VINA

Software

PQB2PQR, Javaplex, R-TDA, Scikit-learn

Parameters

NA

Method

Machine learning based method using the selected top poses.

Answer 1

No

Name

Align_target/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.

Pose Prediction Parameters

Solvation model = VSGB
Force field = OPLS3
Refine atoms within 10.0 \AA of ligand
Sampling algorithm = Local optimization

Pose Prediction Method

Each target ligand is aligned to its most similar structure available in Protein Data Bank. The algined ligand is optimized to the binding site of the receptor using Prime in Schrodinger.

Answer 1

No

Answer 2

Yes