Antibody Visualization¶
Visualize a structure that contains an antibody or an antigen using our preset.
Inputs & Parameters¶
To submit an Antibody Visualization job, open the Project Editor and select "Antibody Visualization" from the "Preprocessing" dropdown menu.
Inputs to this job include:
- Structure: Choose a PDB or mmCIF file from the project that contains an antibody or an antigen.
- Heavy chain (Optional): Choose one heavy chain ID from the structure to visualize. If not specified, no heavy chain will be displayed.
- Light chain (Optional): Choose one light chain ID from the structure to visualize. If not specified, no light chain will be displayed.
- Antigen chain (Optional): Choose one antigen chain ID from the structure to visualize. If not specified, no antigen will be displayed.
Parameters to this job include: - CDR def.: Numbering scheme used for definition of CDR regions. Could be either "Kabat", "IMGT", "Chothia", "North".
Chain type identification
GeoBiologics will automatically classify each chain in the structure as "heavy chain", "light chain" or "antigen". If the classification is incorrect, please contact us or submit a feedback.
Results¶
This job will not generate a job record in the Files & Jobs panel. Instead, the chosen structure will be open and visualized in the Structure Viewer immediately after submission.
Structural components will be created and represented as follows:
- Polymer: Default component that contains all polymer in the structure. It will be hidden by default.
- antibody: Selected heavy and light chains. If neither heavy nor light chain is selected for visualization, this component will not be created. If created, it will be represented by:
- A Molecular Surface representation with transparency of 0.25, colored by hydrophobicity, with cyan indicating hydrophilic and yellow indicating hydrophobic.
- antigen: Selected antigen chain. If no antigen is selected for visualization, this component will not be created. If created, it will be represented by:
- A Molecular Surface representation with transparency of 0.25, colored by hydrophobicity, with cyan indicating hydrophilic and yellow indicating hydrophobic.
- A Cartoon representation with purple color.
- heavy chain: Selected heavy chain. If no heavy chain is selected for visualization, this component will not be created. If created, it will be represented by:
- A Cartoon representation with blue color.
- light chain: Selected light chain. If no light chain is selected for visualization, this component will not be created. If created, it will be represented by:
- A Cartoon representation with orange color.
- HCDR: CDR regions of the selected heavy chain. If no heavy chain is selected for visualization, this component will not be created. If created, it will be represented by:
- A Cartoon representation with light blue color.
- LCDR: CDR regions of the selected light chain. If no light chain is selected for visualization, this component will not be created. If created, it will be represented by:
- A Cartoon representation with light orange color.
- epitope: Epitope of the selected antigen chain, calculated as all antigen residues within 5Å of the selected antibody. Both antibody and antigen must be present for the creation of this component. If created, it will be represented by:
- A Ball & Stick representation with purple color.
- Hparatope: Paratope of the selected heavy chain, calculated as all heavy chain residues within 5Å of the selected antigen. Both antibody and antigen must be present for the creation of this component. If created, it will be represented by:
- A Cartoon representation with blue color.
- Lparatope: Paratope of the selected light chain, calculated as all light chain residues within 5Å of the selected antigen. Both antibody and antigen must be present for the creation of this component. If created, it will be represented by:
- A Cartoon representation with orange color.
- interface: Interface between the selected antibody and antigen. Both antibody and antigen must be present for the creation of this component. If created, it will be represented by:
- A Non-covalent Interactions representation, where hydrogen bonds are represented by blue lines, hydrophobic interactions by grey, halogen bonds by teal, ionic interactions by yellow, metal coordination by , cation-pi interactions by orange, pi-stacking interactions by lime, and weak hydrogen bonds by blue grey.
Feel free to hide or show these components at will. You may also change the representations of each component to suit your needs.