k84ej-LigandScoringProtocol.txt

Name

corina-smina-HYDE

Software

HYDE (SeeSAR 2016-12-08)

Parameters

default

Method

Generated poses were scored with HYDE as implemented in SeeSAR.

Answer 1

No

k84ej-PosePredictionProtocol.txt

Name

rdkit-smina-hyde

Software

ProPKA/Chemaxon/rdkit/MGLTools/Smina Apr 2 2016. Based on AutoDock Vina 1.1.2./SeeSAR 2016-12-08

System Preparation Parameters

Assumed pH 7.4
Protonation states > 25% considered
Gasteiger charges

System Preparation Method

ProPKA was used to add hydrogens using default parameters.
No water molecules were retained while GAFF force field parameters were assigned to the proteins (CAT1 with and without SO4 and CAT2 with DMSO).
Ligand were protonated using Chemaxon. Each protonation state >25% at pH7.4 was considered. The ligands 3D conformation was generated with rdkit (ETKDG).
Preparation for docking with Smina was done using MGLTools where the ligand were converted to PDBQTs by assigning charges and atom types. Generated poses were scored with HYDE as implemented in SeeSAR.

Pose Prediction Parameters

smina was run with the following parameters : scoring = vinardo, num_modes = 60, exhaustiveness = 32; minimize_iters = 100

Pose Prediction Method

Poses were generated with smina. Pose were optimized with ProToss and HYDE as implemented in SeeSAR and scored with HYDE as implemented in SeeSAR. Poses ranked 1st with SeeSAR were selected. No visual inspection was used for pose selection.

Answer 1

No

Answer 2

No