Antibody CDR Loop Ensemble Generation

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

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

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

Description

This floe generates an ensemble of loop conformers for a selected loop region on the input antibody design unit. Conformers are generated using the OEBuildSingleLoop function, and CDR regions will be automatically detected and numbered using the specified numbering scheme. To run loop generation on any nonCDR regions, see the related floes.

Limitations: For a given floe run, only one CDR loop can be selected for loop building.

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

Related Floes: Protein Loop Modeling or Re-modeling

Promoted Parameters

Title in user interface (promoted name)

Loop Building Parameters

CDR Selection (cdr_selection): Select CDR loop for modeling

  • Type: string

  • Default: HCDR3

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

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

  • Required

  • Type: string

  • Default: IMGT

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

Loop Crop Length (crop_length): Anchor residues on the protein to crop back for a better fit, results in longer loops being built.

  • Required

  • Type: integer

  • Default: 1

Number of Loops to Minimize and Evaluate (numbering_smax_eval_loopscheme): Maximum number of loops to connect and minimize.

  • Required

  • Type: integer

  • Default: 5

Outputs

Output Ensemble Fv (out): Loop ensembles of annotated Fv design units are output to a dataset.

  • Required

  • Type: dataset_out

  • Default: CDR Loop Ensemble

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

  • Required

  • Type: dataset_out

  • Default: failed_CDR Loop Ensemble