Protein Structure Visualization and Ligand Docking Digital Badge

Contact Information

The Protein Structure Visualization and Ligand Docking badge is a competency badge offered through the Department of Chemistry and Biochemistry. Completing this badge demonstrates foundational knowledge in the use of the Protein Data Bank (PDB) to obtain information about protein structures, customize visualizations of the proteins, and use docking models to understand protein-ligand interactions.

Earning Criteria

Participants earning this badge are required to demonstrate effective use of the Protein Data Bank (PDB) website, describe the contents of a PDB text file, analyze a protein structure, create a customized image of a protein, and predict and interpret protein-ligand interactions by creating a docking model.

Competencies Demonstrated

1. Provide resolution and method of determining structure for a given Protein Data Bank (PDB) entry.
2. Describe general levels of detail that can be seen at different levels of resolution.
3. Identify publication associated with structure.
4. Provide residue identifier names for non-protein molecules in structure.
5. Explain what details are provided by the atom coordinate line in a PDB text file.
6. Customize colors of specific residues.
7. Adjust representation of atom type and secondary structure backbone of specific parts of protein.
8. Select region based on distance to atom and customize display.
9. Measure distance between atoms.
10. Save publication quality images with orientation to see important features.
11. Save structure viewer session file.
12. Identify molecules that could be used to mimic natural substrate and describe how differences and similarities may affect interaction with the receptor protein.
13. Explain features of “best” conformation from a docking model output and why it was selected.
14. Describe significance of alternative conformations.