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, e.g. molecular dynamics based approaches.While cost effective, it should be noted that depending on the calculation the results could be affected bysimulation a monomer instead of a dimer, so this cannot be recommended as a general strategy

Parameter title in user interface (promoted name)

  • Solvent within distance (dist) type: decimal: The heavy atom distance threshold used to determine whether to retain a water moleculedistance is to the subset of the design unit kept based on the binding site chain IDs
    Default: 5.0

Parameter title in user interface (promoted name)

  • 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

Parameter title in user interface (promoted name)

  • Within Components (within_choices) type: string: Components to calculate distance to for the solvenet 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

Parameter title in user interface (promoted name)

  • Output Dataset (data_out) type: dataset_out: Dataset with modelled design unit.
    Default: Binding Unit DesignUnits

Parameter title in user interface (promoted name)

  • Failure Dataset (data_out) type: dataset_out: Dataset with design unit that failed to be successfully modelled.
    Default: failed_Binding Unit DesignUnits

Parameter title in user interface (promoted name)

  • Input Design Unit (data_in) type: data_source: Dataset with design unit(s) to be modelled