corina-smina-HYDE
HYDE (SeeSAR 2016-12-08)
default
Generated poses were scored with HYDE as implemented in SeeSAR.
No
corina-smina-hyde
ProPKA/Chemaxon/Corina/MGLTools/Smina Apr 2 2016. Based on AutoDock Vina 1.1.2./SeeSAR 2016-12-08
Assumed pH 7.4
Protonation states > 25% considered
Gasteiger charges
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 Corina (https://www.mn-am.com/online_demos/corina_demo).
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.
smina was run with the following parameters : scoring = vinardo, num_modes = 60, exhaustiveness = 32; minimize_iters = 100
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.
No
No