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, Chothia, 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 including motifs associated with post and co-translational modifications. 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]