Rhodium HTS CELPP xxxxx method
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
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 binding site residues were fixed as were the conformers used in the rigid-body docking.
Parameters are identical to entries used to date in the CELPP contest by user xxxxx, up to week 39.
Rhodium HTS method using default parameters of: 72 trial poses per grid point, per conformer, and exactly 8 poses refined for each conformer.
The guided style of docking was used, specifying docking location by center of mass of other cathepsin-s inhibitors crystallized in the Protein Databank.
Identical to entry xxxxx in CELPP. 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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