corina-smina-HYDE
HYDE (SeeSAR 2016-12-08)
default
Generated poses were scored with HYDE as implemented in SeeSAR.
No
rdkit-rDock_const-hyde
ProPKA/Chemaxon/rdkit/MGLTools/rDock/SeeSAR 2016-12-08
Assumed pH 7.4
Protonation states > 25% considered
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).
rDock generated poses were scored with HYDE as implemented in SeeSAR.
definition of the cavity 6A around the ligand from structure 3iej / 50 poses generated / pharmacophoric constraints on hydrophobic features embedded in the binding site for ligands of structures 3mpe 3iej and 3kwn : 4.33 9.96 -8.12 2.0 Har; 5.51 7.42 -4.82 2.0 Har; 5.91 5.51 -2.86 1.25 Hyd / Flexible binding site (receptor flex = 3.0A)
Poses were generated with rDock with constraints on pharmacophoric features common to 3 co-cristallized ligands similar to the D3R ligands. 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