Rhodium 5.8 HTS
Pymol 1.2
Accelerys Discovery Studio 2.0
Rhodium 5.8
OpenBabel 2.3.90
Caesar 3D Conformers with Default Parameters
Pymol was used to add hydrogens to crystal structures using default parameters.
All the waters were removed.
Ligand conformational libraries were generated using the Casear method in Discovery Studio 2.0 with default parameters, for all but two ligands.
All conformers were used in the docking. BACE_2 and BACE_3 were created from SMILES strings using OpenBabel 2.3.90, and optimized with the obminimize program. PDB files were unmodified except for the addition of hydrogen atoms.
Rhodium HTS Default Parameters
Grid Resolution 1.7 #exhaustiveness of global search (default=2.0)
NumPoses 144 #max number of poses to generate
Docking runs were executed with the above specified parameters, using approximately 50 crystal structures of BACE.
Structures were selected based on docking score, considering all poses in all crystal structures.
The topmost-scoring pose of each ligand from the Rhodium docking is submitted with this protocol.
No
Yes