PoPSS-PB
Omega 3.0.0.1
ROCS 3.2.2.2
Szybki 1.9.0.3
A maximum of 2000 conformations per ligand were generated using macrocycle mode of Omega
RefTverskyCombo coefficient was used for evaluating shape similarity
Ligand conformations for shape similarity calculations were generated using macrocycle mode of Omega. A maximum number of 2000 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 within active site considering solvent effects. Ligand conformations were generated using Omega program. All available ligand bound crystal structures of BACE-1 from PDB were downloaded and were superimposed onto BACE-1 crystal structure (PDB code 5YGX). 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 Szybki pose refinement considering solvent effects. Poisson–Boltzmann model was used for solvent effects. Protein structures for were selected based on ROCS shape similarity calculation and the structures with highly shape similar crystal ligand was used. Protein residues within 5 Angstrom of ligands atoms with utilized in refinements while rest of the protein residues were kept rigid.
Yes
Yes