SZYBKI - Ligand Minimization in a Rigid Active Site
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Product-based/SZYBKI
Solution-based/Small Molecule Lead-opt
Task-based/Ligand Posing & Analysis
Role-based/Computational Chemist
Description
SZYBKI - Ligand Minimization in a Rigid Active Site optimizes ligands in a fixed protein active site. Only the ligand is modified, while the protein is kept fixed during the optimization.
The minimal input into Classic Szybki Ligand in Fixed Protein is a design unit or a 3D protein structure, and a dataset of molecules in 3D format.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Input DU/Ligand (in): Dataset containing design units or ligands to optimize. For ligand inputs, a second dataset of a Design unit must also be provided.
Required
Type: data_source
Input Design Unit (init): (Optional) Dataset containing design unit for docked ligands. An entry in this field assumes that ligands from the other dataset to be optimized against protein from this DU.
Type: data_source
SZYBKI settings
Components to keep as the ‘protein’ (protein_mask): DU components to use as the ‘protein’.
Type: string
Default: [‘protein’, ‘nucleic’, ‘cofactors’, ‘solvent’, ‘other_ligands’, ‘other_cofactors’]
Choices: [‘protein’, ‘nucleic’, ‘ligand’, ‘solvent’, ‘metals’, ‘counter_ions’, ‘lipids’, ‘packing_residues’, ‘sugars’, ‘undefined’, ‘cofactors’, ‘excipients’, ‘polymers’, ‘post_translational’, ‘other_proteins’, ‘other_nucleics’, ‘other_ligands’, ‘other_cofactors’]
Force Field (force_field): Built-in force field model to be used.
Type: string
Default: ff14sb_sage
Choices: [‘ff14sb_sage’, ‘ff14sb_parsley’, ‘mmff94’, ‘mmff94s’, ‘mmff_amber’, ‘mmffs_amber’]
Custom FF File (ff): Custom smirnoff force field file. Entry in this field creates a OEFF14SBSmirnoff force field and overrides any other force field selections
Type: file_in
Solvent model (solvent_model): Solvent model to be used
Type: string
Default: Gas-phase
Choices: [‘Gas-phase’, ‘Sheffield’, ‘PB’]