Omega/ROCS/Glide-Refine
Omega 2.5.1
ROCS 3.2.0
Glide 6.1
A maximum of 1000 conformations per ligand were generated
RefTverskyCombo coefficient was used for evaluating shape similarity
Ligand conformations for shape similarity calculations were generated using Omega. A maximum number of 1000 conformations per ligand was generated. Receptors were prepared using protein preparation utility of Maestro.
None
This method places a ligand conformation with highest 3D shape similarity with known crystal structure ligand into protein binding site and then refines the pose by performing energy minimization. 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 Glide-SP refine only protocol. Protein structures for were selected based on ROCS shape similarity calculation and the structures with highly shape similar crystal ligand was used.
Yes
Yes