Workshop: Analyzing 3D PDB structures.


Jupyter notebook

Learning resources


A PDB structure of a protein with at least two domains will be suggested for analysis. The assignment report should include section detailing the following:

  1. Protein dihedral angle analysis
  2. Contact maps
  3. Identify domains
  4. Find homologous structural domains, compute RMSD
  5. Identify protonation states of ionizable residues
  6. Surface analysis
    • identify polar, charge, hydrophopic residues on the surface
    • visualize electorstatic potential at the surface using PDB2PQR and APBS
  7. Dynamics analysis
  8. Conservation analysis

Suggested problem sets

Each student should take a unique PDB structure with at least two domains from the PDB web-site at his/her own discretion.