Antibody Structure Relaxation

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

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

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


This floe performs structure relaxation (minimization) on input antibody design units. Only the selected regions on the design unit will be flexible during relaxation. Minimization uses OEFF functionality to relax the antibody design unit.

Potential Input Sources: Antibody Sequences to 3D Models Floe, Antibody Experimental Structure Prep Floe

Related Floes: Minimize Design Unit

Promoted Parameters

Title in user interface (promoted name)

Minimization Parameters

Sequence Numbering Scheme (numbering_scheme): This parameter sets the numbering scheme applied to antibodies.

  • Required

  • Type: string

  • Default: IMGT

  • Choices: [‘IMGT’, ‘Chothia’, ‘Martin’, ‘Kabat’]

Run Minimization (run_minimize): Option to run structure minimization.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

CDR Selection (cdr_selection): CDR loop regions to be flexible during structure relaxation.If none are selected entire system is marked flexible

  • Type: string

  • Default: [‘HCDR3’, ‘HCDR2’, ‘HCDR1’, ‘LCDR3’, ‘LCDR2’, ‘LCDR1’]

  • Choices: [‘HCDR3’, ‘HCDR2’, ‘HCDR1’, ‘LCDR3’, ‘LCDR2’, ‘LCDR1’]

Make specified residue atoms flexible (flex_residues): Allow the atoms in the specified residues to be flexible for the minimization (format is RESNAME:RESNUM:ICODE:CHAINID[:FRAGNO:ALTLOC] - separate multiple with | delimiter.

  • Type: string

Flexible atom predicate (minimize_pred): Predicate to define what atoms to be flexible during the minimization, this will subset the flexible (site-)residues. Multiple selections work as OR statements.

  • Required

  • Type: string

  • Default: [‘All atoms’]

  • Choices: [‘All atoms’, ‘Heavy atoms’, ‘H atoms’, ‘Polar H atoms’, ‘Methyl H atoms’, ‘Backbone atoms’]


Output Minimized Fv (out): Dataset with minimized design units.

  • Required

  • Type: dataset_out

  • Default: MinimizedDesignUnits

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

  • Required

  • Type: dataset_out

  • Default: failed_MinimizedDesignUnits