Molecular similarity/ ligand alignment
RDkit (2018.03.4) / MOE (2018.0101)
Default MOE parameters
None
Default MOE parameters
A total number of 269 BACE-1 complex structures were first downloaded from the PDBbind website. After removing the peptide-like ligands, the size of this dataset was reduced to 261, which we call the PBNP (PDBbind-BACE-Nonpeptide) dataset. The molecular similarities between the target ligands (D3R ligands) and the crystal ligands in the PBNP dataset were then calculated using the circular fingerprints (ECFP4) generated via RDKit. It was observed that one of the complex structures in the PBNP dataset, 3DV1, contains a macrocycle ligand which has a moderate to high similarity with most of the target ligands. Therefore, the 3D conformations of the D3R ligands were generated and aligned with the 3DV1 ligand, which were subsequently superimposed to the receptor structures provided by the organizers. The crystallographic waters in the crystal structures of the receptors were preserved during minimization and docking.
No
Yes