Rhodium HTS
Rhodium 380E9-X9/ Openbabel 2.3.90 / pymol 1.3
Docking resolution 1.7 A
Number of poses minimized per conformer : up to 144
Number of conformers per ligand: 30
Scoring method: KRh Scorpio, from poses of maximum cavity filling (Rhodium CAVOC)
Scoring function: Regression model using training set from SCORPIO database
Pymol was used to add hydrogens to pdb protein models using default parameters.
Rigid-body ligand conformational libraries were generated using openbabel to produce and optimize 3d structures with the MMFF94 forcefield.
Conformers were produced with the GA method using default parameters. Conformers were re-optimized with the MMFF94 forcefield.
All binding site residues were fixed as were the conformers used in the rigid-body docking.
Several available crystal structures of the kinase target were docked with the Rhodium HTS method
For each ligand, poses of maximum cavity filling (by Rhodium CAVOC score) were selected from a manifold of minimzed poses.
Ligands were ranked with a score called "KRh Scorpio" previously derived from a training set consisting of holo crystal structures and ITC free energy in the SCORPIO database.
No
Rhodium HTS
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
Protein pdb files prepared with pymol by adding H atoms
Pymol was used to add hydrogens to pdb protein models using default parameters.
Ligand 3d structures were created with openbabel using the MMFF94 forcefield for minimization.
Rigid-body ligand conformational libraries were generated using openbabel GA method with default parameters, and the resulting conformers were re-optimized with the MMFF94 forcefield
All binding site residues were fixed as were the conformers used in the rigid-body docking.
Several available crystal structures of the kinase target were docked with the Rhodium HTS method.
Rhodium HTS method. Poses of maximum cavity filling (by Rhodium CAVOC score) were selected for each ligand from a manifold of minimzed poses.
Poses were selected based on the best score called "KRh Scorpio" previously derived from training set consisting of holo crystal structures and ITC free energy in the SCORPIO database.
No
Yes