Subset Design Unit to Smallest Binding Unit

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/SPRUCE

  • Role-based/Computational Chemist

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation/Structural Data Preparation

  • Task-based/Target Prep & Analysis/Protein Preparation

Description

This floe reduces a design unit to the smallest unit based on the binding site residue location. Thus, if the design unit is a dimer and the design unit binding site is in chain A, it will remove chain B. This makes the unit smaller, which can be cost effective for certain types of calculations, such as molecular dynamics based approaches. While cost effective, it should be noted that depending on the calculation, the results could be affected by simulation of a monomer instead of a dimer, so this cannot be recommended as a general strategy.

Titles of required parameters (promoted names)

  • Solvent within distance (dist) type: decimal: The heavy atom distance threshold used to determine whether to retain a water molecule.
    Default: 5.0
  • Retain solvent close to primary unit, but with different chain IDs (retain_solvent) type: boolean: Retains solvent within a threshold distance of the primary unit.
    Default: True
  • Within Components (within_choices) type: string: Components near to the binding site used calculate distance to for the solvent subset
    Default: [‘protein’, ‘nucleic’, ‘ligand’, ‘cofactors’, ‘other_proteins’, ‘other_nucleics’, ‘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
  • Output Dataset (data_out) type: dataset_out: Dataset with modelled design unit.
    Default: Binding Unit DesignUnits
  • Input Design Unit (data_in) type: data_source: Dataset with design unit(s) to be modelled
  • Failure Dataset (data_out) type: dataset_out: Dataset with design unit that failed to be successfully modelled.
    Default: failed_Binding Unit DesignUnits