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