Antibody Subset System

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/Hit to Lead/Target Preparation/Structural Data Preparation

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Biologics/Antibody Design/Target Preparation

Description

In this floe, only the indicated parts of the input antibody design unit are subset using OESubsetDesignUnit function.

Potential Input Sources: Antibody Experimental Structure Prep Floe

Related Floes: Subset Design Unit

Promoted Parameters

Title in user interface (promoted name)

Subset Parameters

Components to keep in the subset (subset_choices): Different components to keep in the subset.

  • Required

  • Type: string

  • Default: [‘protein’, ‘nucleic’, ‘ligand’, ‘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’]

Delete molecule component (delete_pieces): Delete entire molecule component containing specified residues. Format: ‘RESNAME:RESNUM:ICODE:CHAINID[:FRAGNO:ALTLOC]’, e.g. ‘ALA:325: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard. Separate multiple with ‘|’ delimiter.

  • Type: string

Delete Residues (delete_residues): Delete specified residues. Format: ‘RESNAME:RESNUM:ICODE:CHAINID[:FRAGNO:ALTLOC]’, e.g. ‘ALA:325: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard. Separate multiple with ‘|’ delimiter.

  • Type: string

Convert R-groups to Hydrogen atoms (r2h): Convert R-groups from broken covalent bonds due to deleted pieces to Hydrogen atoms.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Outputs

Output Subset Design Units (out): Dataset with design units that have been subset to keep only the desired components.

  • Required

  • Type: dataset_out

  • Default: SubsetDesignUnits

Failure Dataset (failed_dataset): Dataset with design unit that failed to be successfully modelled.

  • Required

  • Type: dataset_out

  • Default: failed_SubsetDesignUnits