Name

Alignment/AlphaSpace/Smina

Software

RDKit(2018.3.3)/Smina(2017.4.29)/MGLTools(1.5.6)/OpenBabel(2.4.1)/AlphaSpace(1.1.10)/PDB2PQR(2.1.0)

System Preparation Parameters

pdb2pqr --ff=amber --ph-calc-method=propka --with-ph=5

System Preparation Method

1. Receptor preparation: PDB2PQR was used to calculate receptor protonation states and hygrogen atoms are added accordingly. 2. Ligand preparation: a. Conformer library was generated using RDKit. b. Ligand protonation states were calculated using in-house script, which was developed by functional group potonation states at specific conditions. 3.Ligand and receptor pdbqt files are prepared by MGLTools.

Pose Prediction Parameters

smina --minimize --minimize_iters=100

Pose Prediction Method

1. Morgan fingerprints were used to select most similar cocrystal ligand for each GC4 compound. 2.Generated conformers were aligned to its most similar cocrystal ligand using MCS (Most Common Substructures) in RDKit. 3. Aligned conformers were local minimized against its most similar cocrystal ligand's receptor using Smina. 4. AlphaSpace was used to analyze available CatS crystal structures in PDB, and major pocekts were determined by AlphaSpace pocket space and ligandability. 5.Minimized conformers were filtered by their major pocket space occupancy 6. Top Smina score conformer was selected as predicted pose.

Answer 1

No

Answer 2

Yes

Name

Smina

Software

Smina 2017.4.29

Parameters

Default parameters.

Method

Smina scores of the selected poses based on docking protocol Alignment/AlphaSpace/Smina were used as predicted scores.

Answer 1

No

Answer 2

No