Antibody Experimental Structure Prep

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

  • Role-based/Structural Biologist

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation/Structural Data Preparation

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

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

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

Description

This floe uses Spruce to generate an OEDesignUnit that has be styled and annotated for use in antibody applications and downstream modeling.

At least one input is required to run this floe and can come from one or more of the following input types: (1) PDB or MMCIF files accompanied by MTZ files with electron density maps (if available). (2) A valid PDB code. Multiple PDB codes may be submitted using a CSV string.

Heavy and light chains will be identified from the structure’s sequence data and renamed accordingly. A naming scheme (from a selection of IMGT, Cothia, Martin, or Kabat) will be applied to the antibody’s residues and renumbered. The design unit’s styling will identify the different CDR regions and label the structure’s liabilities. If antigens are present in the experimental structure, these will be classified as Other Proteins.

By default, patch analysis will also be run on the structure. Patch analysis defines patch surface(s) based on hydrophobicity and/or charge and can optionally calculate SZMAP surfaces. Additional styling shows all residues that are in proximity to the default hydrophobic patch method.

Limitations: Currently, only experimental Fv structures are supported for input. Any structures where an Fv is not present will fail the floe.

Related Floes: Antibody Surface Patch Generation, Antibody Sequences to 3D Models, Antibody Subset System, and Antibody MD Simulations with Conformational Analysis Floes, SPRUCE - Protein Preparation

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

Inputs

PDB files to prepare (file_cube_in): PDB files to prepare for Ab modeling.

  • Type: file_in

Input electron density map (MTZ) files (mtz_files): Map file name must have the same root as its associated structure (PDB/MMCIF) file. If provided, floe will ensure that the density map(s) are paired with a coordinate file.

  • Type: file_in

PDB codes to prepare (code_cube_in): PDB codes to prepare for Ab modeling.

  • Type: string

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

  • Required

  • Type: string

  • Default: IMGT

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

Style Liabilities (style_liabs): Option to style known liability patterns.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Outputs

Output Dataset of Antibody Structures (out): Output dataset to write to

  • Required

  • Type: dataset_out

  • Default: Exp_Antibody_Structures

Failed Structure Output (failed_out): Output dataset to write to

  • Required

  • Type: dataset_out

  • Default: failed_input_structures

Loop Builder Parameters

Build missing loops (build_loops): Option to build missing loops (if information is available to do so)

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Build Missing Tails (build_tails): Option to build missing tails (if information is available to do so)

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]