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PDB Files

The PDB Files view allows you to manage and visualize 3D structural models associated with your project.

This tool is useful for inspecting the sequences extracted from PDB files, matching them to your entry sequences, downloading or deleting selected PDB files, and visualizing the 3D structures.

Accessing the Tool

Go to the Edit menu in the Project View and select PDB Files. This will open the PDB Files interface in a new tab.

PDB Files

Using the Tool

  • PDB Filename: Displays the name of the PDB file. Clicking the button to the left of the filename toggles the 3D structure viewer.
  • 3D Structure Viewer: Click the toggle button to open/close the Molstar window at the bottom of the page to visualize the 3D structure. The backbone is colored by region (FMWK, CDRs) using the project's color system. Residues and side chains are not displayed to keep the view clean.
  • Draggable Pane: The viewer pane can be resized by dragging the handle at the top of the pane.
  • Extracted Sequences: Displays the sequences extracted from the PDB file, broken down by chain. Residues that match the entry sequence are highlighted.
  • Download Selected: Select one or more entries and click to download a ZIP file containing the PDB files.
  • Delete Selected: Select one or more entries and click to remove the PDB files from the entries. This does not delete the associated entries.

While AbLead can be used as a PDB repository, for more robust solutions consider using JStruct or commercial products like Molecular Operating Environment's PSILO.

References

  • PDBe Mol* is used for 3D structure visualization. See Mol* for details.
  • ABodyBuilder2 (ImmuneBuilder) is described in ImmuneBuilder on GitHub.