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: Determined by Confab method of openbabel, with energy cutoff of 4 and up to 90 million conformers sampled.
Scoring method: Rhodium CAVOC score, from poses of maximum cavity filling (Rhodium CAVOC)
Scoring function: Rhodium CAVOC
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 confab package, using an energy cutoff of 4 and up to 90 million conformers sampled.
All binding site residues were fixed as were the conformers used in the rigid-body docking.
Several homology structures of the kinase targets were docked with the Rhodium HTS method. Homology models were made with SwissModel, using the website accessed in November 2017.
For each ligand, poses of maximum cavity filling (by Rhodium CAVOC score) were selected from a manifold of minimzed poses.
Ligands were ranked by the CAVOC score.
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 confab method, using an energy cutoff of 4 and up to 90 million trial conformers searched.
Ligand conformers further optimized by openbabel obminimize
Protein pdb files were made by homology modeling using SwissModel website, accessed November 2017.
Protein pdb files were 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.
All binding site residues were fixed as were the conformers used in the rigid-body docking.
Several homology models 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 maximum CAVOC
No
Yes