Visualizing structural biology: an interactive introduction

  1. Introduction 
    About this tutorial. Installation. Technical issues and requirements.
  2. Molecular visualization: the PDB and PyMOL
    Overview of the PDB: what is in it? How to use it? Starting with PyMOL.
  3. Exploring a globular protein: Myoglobin
    Learn about general structures of proteins by exploring Myoglobin. Explore the basic biochemical properties of the molecule and find the connections with the actual structure. Get into the basics of using PyMOL for molecular visualization: mouse controls, objects and selections.
  4. Enzymatic catalysis: Citrate Synthase
    Understand binding events and enzymatic catalysis at a structural level. More on mouse controls, objects, and advanced selections in PyMOL. Structural superimposition to explore protein dynamics.
  5. Membrane proteins: Bacteriorhodopsin
    What is particular about membrane proteins, in comparison with non-membrane ones? Study the case of Bacteriorhodopsin. Learn the command line input mode of PyMOL. It has benefits in reproducibility of scenes and automation of tasks. 
  6. Molecular recognition
    Protein complexes and DNA - protein complexes are studied as the first step towards the rational design of new molecules to modulate cell-function. More complex tasks with the command line. Learn how to make publication-quality pictures with PyMOL.
  7. NMR structures vs X-Ray structures
    Learn differences between X-ray structures and NMR structures in the PDB. Advanced PyMOL concepts: scripts for automation of tasks. Movies.
  8. Self-assessment exercises

This tutorial has been developed at the Molecular Bioinformatics Laboratory - Heinrich-Heine-Universität Düsseldorf