yetdj-PosePredictionProtocol.txt

Name

PoPSS

Software

Omega 2.5.1
ROCS 3.2.0
Rosetta Suite 2015.25

System Preparation Parameters

A maximum of 1000 conformations per ligand were generated
RefTverskyCombo coefficient was used for evaluating shape similarity

System Preparation Method

Ligand conformations for shape similarity calculations were generated using Omega. A maximum number of 1000 conformations per ligand was generated. Receptors for docking were prepared using fast_relax protocol of Rosetta.

Pose Prediction Parameters

None

Pose Prediction Method

Our method PoPSS amalgamates ligand 3D shape similarity with RosettaLigand "high resolution" docking. PoPSS place a ligand conformation with highest 3D shape similarity with known crystal structure ligand into protein binding site and then refines the pose by repacking the side chain and performing energy minimization with a Monte Carlo algorithm. Ligand conformations were generated using Omega program. All available ligand bound crystal structures of Cathepsin S and other homologous proteins from PDB were downloaded and were superimposed with target protein. Relevant ligands were extracted and ligand 3d shape similarity calculations between ligand conformations and crystal structure ligand were performed. Shape similarity calculations were performed using ROCS. Top scoring ligand conformation for each ligand was placed into target protein binding site and refined using "high resolution" docking option of Rosettaligand. Protein structures provided for Stage 1b were used for respective ligands. Two hundred poses were generated that were sorted using "interface delta" score. Pose with best "interface delta" score was selected as final pose.

Answer 1

Yes

Answer 2

Yes