qokw3-LigandScoringProtocol.txt

Name

xScore

Software

Glide, Gold, xScore

Parameters

with optimization

Method

Each compounds was docking using Glide and Gold to its closest xray(most simlar to the ligand); A protein-ligand interaction fingerprints was used to select the best pose; Finally, the pose was scored using xScore. xScroe from this paper:Comparative Evaluation of Eleven Scoring Functions for Molecular Docking J. Med. Chem. 2003, 46, 2287-2303.

qokw3-PosePredictionProtocol.txt

Name

Glide/Gold/xScore

Software

Schrodinger/2016-3, CCDC/5.4.0, xScore

System Preparation Parameters

Ligands were prepared at pH 7.4 +/- 0.0. The stereochemistries were given in the isosmiles strings and were therefore kept. Proteins were prepared in the following manner: bond orders were assigned, hydrogen atoms added, disulfide bonds were generated, and water orientations were sampled. The charge states were kept at pH 7.0. Missing loops and side chains were constructed. The given residue confirmations were kept, with no alternative residue conformations examined.

System Preparation Method

Schrodinger ligand preparation and protein preparation wizard

Pose Prediction Parameters

The pose predictions in this set were docked using a protocol to examine the ligand similarity to known structures, and docked using Schrödinger'ss Glide or CCDC Gold.

Pose Prediction Method

Upto 5 poses were generated by Glide and Gold. All the poses were ranked by protein-ligand finger prints and the top one was chosen for scoring using xScore.