Rhodium HTS Guided
Rhodium 380E9-X9/Openbabel 2.3.90 / pymol 1.3
Ligand SMILES to sdf by openbabel --gen3D
Ligand sdf optimization by openbabel obminimize -n 20000 -ff MMFF94
Ligand conformers generated by openbabel GA method
Ligand conformers further optimized by openbabel obminimize using default parameters
Protein pdb files prepared with pymol by adding H atoms
Pymol was used to add hydrogens to pdb protein models provided in Stage 1b, using default parameters.
Rigid-body ligand conformational libraries were generated using openbabel GA method with default parameters.
All conformers were then geometry-optimized with the obminimize program, using default parameters and the MMF94 forcefield
All binding site residues were fixed as were the conformers used in the rigid-body docking.
Rhodium HTS method using default parameters of: 72 trial poses per grid point, per conformer, and exactly 32 poses refined for each conformer.
The guided style of docking was used, specifying center of mass of other cathepsin-s inhibitors crystallized in the Protein Databank.
This center was included as a single entry in the RHODIUM.GRID file to initiate the docking search.
After docking each conformer in its cognate crystal structure. The best pose of each ligand, by docking score, was selected based on the best score, after "self" docking using the crystal structures provided
The topmost scoring pose was selected, following automatic elimination of crowded poses as identified by Rhodium's default crowding detection method.
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