Antibody Surface Patch Generation

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/SPRUCE

  • Product-based/SZMAP

  • 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/CDR Analysis

  • Solution-based/Biologics/Antibody Design/Target Preparation/Surface Patch Analysis

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

Description

Takes a dataset of antibody design units as input and defines patch surface(s) based on hydrophobicity and/or charge, and can optionally calculate SZMAP surfaces. By default, the antibody will be re-styled to show all residues that are in proximity to the default hydrophobic patch method.

Antibody structures are also analyzed for structure properties and TAP scores.

Potential Input Sources: Antibody CDR Loop Ensemble Generation, Antibody Mutate Residue(s), Antibody Structure Relaxation, Antibody Subset System

Related Floes: Antibody Sequences to 3D Models Floe, Antibody Experimental Structures Prep

Promoted Parameters

Title in user interface (promoted name)

Patch Analysis Options

Patch and Property Analysis (switch): Option to run patch hydrophobicity and antibody property calculations.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Style DU Based on Hydrophobicity (style_du): All residues that are in proximity to the hydrophobic surface will have the wireframe atom style. If multiple surfaces are detected, the first method/scale pair from the selection menu will be used to style the protein.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Hydrophobic Patch Method(s) (method_names): Sets how hydrophobic patches are calculated. When viewing the patches in the 3D viewer, green are hydrophobic, and purple are hydrophilic patches.

  • Type: string

  • Default: [‘SAP’]

  • Choices: [‘SAP’, ‘SASA’, ‘Sequence’]

Hydrophobic Patch Scale(s) (scale_names): Sets the scaling scheme(s) for hydrophobic patch calculation. All selected scales are dependent on the Hydrophobic Patch Method parameter.

  • Type: string

  • Default: [‘Jain’]

  • Choices: [‘Jain’, ‘Bandyopadhyaya-Mehler’, ‘Eisenberg’, ‘Meek’, ‘Rose’, ‘Wimley-White’, ‘Miyazawa’, ‘Black-Mould’, ‘Kyte-Doolittle’]

Hydrophobic Patches (style_hydro_patch): Style the hydrophobic surface(s) using patches instead of displaying the entire surface.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Charge Surface Method(s) (charge_method_names): Sets how charged patches are calculated. When viewing the patches in the 3D viewer, red are positively charged, and blue are negatively charged patches.

  • Type: string

  • Default: [‘Formal Charge Electrostatic Potential’]

  • Choices: [‘Formal Charge Electrostatic Potential’, ‘Electrostatic Potential’]

Charge Patches (style_charged_patch): Style the charge surface(s) using patches instead of displaying the entire surface.

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Patch Cutoff (patch_cutoff): Patch cutoff percent of the max value that will be used to identify a patches. Anything below the indicated percent will be cutoff. Values should range between 0.0 and 0.95.

  • Type: decimal

  • Default: 0.4