Schrodinger/2016-3, CCDC/5.4.0, xScore
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.
Schrodinger ligand preparation and protein preparation wizard
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.
Upto 5 poses were generated by Glide and Gold. All the poses from glide and gold were clustering using rmsd 1.0 as cutoff. All the poses were rescoreing using xScore. Best5 poses were chosen.