kazpn-PosePredictionProtocol.txt

Name

vina_HYDE

Software

vina 1.1.2 (may11, 2011) / SeeSAR 2016-12-08 / Open Babel 2.3.2

System Preparation Parameters

Ligand protonation : obabel -p7.4 + manual correction of N-oxide groups / Protein protonation : pdb2pqr --ff amber --ffout amber

System Preparation Method

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

Pose Prediction Parameters

Vina was run with default parameters, 20 poses were generated

Pose Prediction Method

Poses were generated with vina. 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

Yes