Antibody Mutate Residue(s)

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/Structure Prediction

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

Description

This floe performs mutations on input antibody design units. Multiple independent mutations are allowed and are generated using the OEMutateResidue functionality in the order that they appear in the parameter field.

Optionally, and after mutation(s) are completed, functionality in OEFF is used to perform an energy minimization on the antibody structure.

Limitations: Mutations can only be performed on the antibody protein. Mutation on the antigen or any design unit Other Proteins are not allowed at this time.

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

Related Floes: Mutate Residue(s) .html)

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’]

Outputs

Output Mutated Fv (out): Dataset with modelled design unit.

  • Required

  • Type: dataset_out

  • Default: MutatedResiduesDesignUnits

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

  • Required

  • Type: dataset_out

  • Default: failed_MutatedResiduesDesignUnits