Principles of Protein Structure, Comparative Protein Modelling, and Visualisation

Part I: Introduction to Protein structure

• Chapter 1: Secondary Structure and Backbone Conformation
• Chapter 2: Super-Secondary Structure
• Chapter 3: Side Chain Conformation
• Chapter 4: Tertiary Protein Structure and Folds
• Chapter 5: Quaternary Structure

Part II: Protein modelling with SWISS-MODEL

• Help: SWISS-MODEL Workspace Help
• Examples: Protein model example
• Slides: A presentation discussing homology modelling in general

Part III: Model quality

Model quality assessment tools are used to estimate the reliability of predicted protein structure models. The accuracy of individual models may vary significantly from the expected average quality due for instance to suboptimal target-template alignments, low template quality, structural flexibility or inaccuracies introduced by the modeling program. Individual assessment of each model is therefore essential.

• Slides: A presentation discussing model quality

Appendices

• Appendix A: Publications on modelling with SWISS-MODEL
• Appendix B: List of modelling services
• Appendix C: List of model quality assessment tools
• Appendix D: List of protein structure visualization tools

Contributions:

The 5 first chapters of this course (Part I) are adapted from the Internet course on protein structure by J. Cooper, J. Walshaw & Alan Mills.