mol_model_course_2023

Workshop: Analyzing 3D PDB structures.

Description

• Complex analysis of PDB structures
• Duration: 90 minutes
• Objectives: be able to
  • use Pymol and UCSF Chimera programs for analysis
  • do analysis in Python using MDanalysis and Prody libraries
  • select, extract and analyze atom coordinates and dihedral angles.
  • add hydrogens to the structure
  • identify hydrogen bonds
  • identify protonation states
  • assign charges to the atoms
  • compute and analyze electrostatic surface
  • build contact maps
  • identify domains
  • find homologous structures
  • make structural alignment, compute RMSD
  • generate sequence alignment from structural alignment
  • identify residue conservation
  • analyze dynamics using elastic networks models

Jupyter notebook

• 3Dstruct_analysis.ipynb

  Required software and resources

• Pymol, installation instructions
• UCSF Chimera (optional)
• VMD installation link
• Access to a Jupyter notebook evironment with Python 3
• 3-button mouse

List of Conda packages:

• MDanalysis
• nglview
• prody
• propka or use https://www.ddl.unimi.it/vegaol/propka.htm
• pdb2pqr or use https://server.poissonboltzmann.org/pdb2pqr

Channels list (if you use Anaconda Navigator):

• conda-forge
• schrodinger

Learning resources

• MDanalysis tutorial https://www.mdanalysis.org/MDAnalysisTutorial/
• Prody tutorial http://prody.csb.pitt.edu/tutorials/prody_tutorial/
• APBS documentation https://apbs.readthedocs.io/en/latest/

Assignments

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.

Troubleshooting

• Consult with the seminar protocol/recording
• Try to Google, and see Pymol Wiki
• Ask questions in TG