zji7u-PosePredictionProtocol.txt

Name

Rhodium HTS / Center of mass guided

Software

Rhodium 380E9-X9/Openbabel 2.3.90 / pymol 1.3

System Preparation Parameters

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

System Preparation Method

Pymol was used to add hydrogens to pdb protein models 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.
After analysis of a training set, using several docking simulations of known ligands and holo CatS crystal structures, the GC3-provided SO4 bound CatS structure was selected as the best model for
reproducing known ligand pose geometries. Coordinates of the center of mass of known holo ligand poses, aligned to the SO4 structure, were used to locate starting site in the protein for docking.

Pose Prediction Parameters

Rhodium HTS method

Pose Prediction Method

Poses were selected based on the best score. The topmost scoring pose and the pose of maximum cavity-filling (as determined by a cavity-filling metric) were submitted.
This corresponds to pose prediction methods currently submitted to the CELPP challenge with the docking search centered on the expected ligand center of mass, determined from analysis of non-covalent ligands Cat_S in the Protein Data Bank.

Answer 1

No

Answer 2

Yes