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


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)


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’]