rDock_vina_smina_HYDE
vina 1.1.2 (may11, 2011) / rDock 2013.1 / Smina Apr 2 2016. Based on AutoDock Vina 1.1.2. / SeeSAR 2016-12-08 / Open Babel 2.3.2
Ligand protonation : obabel -p7.4 + manual correction of N-oxide groups / Protein protonation : pdb2pqr --ff amber --ffout amber
3D conformations of ligand were generated using obabel. Ligands were protonated with obabel at pH 7.4. N-oxide groups were manually corrected since to attribute correct charge to O- and N+. Protein were protonated with pdb2pqr usinf amber force field parameters
1) 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). 2) Definition of the cavity 6A around the ligand from structure 3iej / 50 poses generated / Flexible binding site (receptor flex = 3.0A). 3) smina was run with the following parameters : scoring = vinardo, num_modes = 60, exhaustiveness = 32; minimize_iters = 100. 4)
1) Poses were generated with rDock with constraints on pharmacophoric features common to 3 co-cristallized ligands similar to the D3R ligands.
2) Poses were generated with rDock with no pharmacophoric constraints.
3) Poses were generated with smina.
4) Poses were generated with vina.
All poses 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
Yes