1. Super-secondary Structure: A Historical Perspective

Michael G. Rossmann

Part I: Representation of Supersecondary Structure

2. Hierarchical Representation of Super-secondary Structures Using a Graph-theoretical Approach

Ina Koch and Annika Kreuchwig and Patrick May

3. Up, Down and Around: Identifying Recurrent Interactions Within and Between Super Secondary Structures in b-Propellers

Søren Thirup, Vikas Gupta and Esben M. Quistgaard

4. Structure Description and Identification using the Tableau Representation of Protein Folding Patterns

Arun S. Konagurthu and Arthur M. Lesk

Part II: Super-secondary Structure Prediction

5. Computational Prediction of Secondary and Supersecondary Structures

Ke Chen and Lukasz Kurgan

6. A Survey of Machine Learning Methods for Secondary and Supersecondary Protein Structure Prediction

Hui Kian Ho, Lei Zhang, Kotagiri Ramamohanarao, and Shawn Martin

7. Beyond Supersecondary Structure: The Global Properties of Protein Sequences

S. Rackovsky

8. Creating Supersecondary Structures with BuildBeta

Silvia Crivelli and Nelson Max

9. A Modular Perspective of Protein Structures; Application to Fragment Based Loop Modeling

Narcis Fernandez-Fuentes and Andras Fiser

10. Residue-residue Contacts: Application to Analysis of Secondary Structure Interactions

Vladimir Potapov, Marvin Edelman, Vladimir Sobolev

Part III: Supersecondary Structure and Protein Folding

11. Super-secondary Structures and Modeling of Protein Folds

Alexander V. Efimov

12. Computational Simulations of Protein Folding to Engineer Amino Acid Sequences to Encourage Desired Supersecondary Structure Formation

Bernard S. Gerstman and Prem P. Chapagain

13. Protein Folding at Atomic Resolution: Analysis of Autonomously Folding Supersecondary Structure Motifs by Nuclear Magnetic Resonance

Lorenzo Sborgi, Abhinav Verma, Mourad Sadqi, Eva de Alba, and Victor Muñoz

14. Artificial Supersecondary Structures Based on Aromatic Oligoamides

Hai-Yu Hu and Chuan-Feng Chen

Part IV: Other Applications of Supersecondary Structure to Protein Biology

15. Cross-b-sheet Super-secondary Structure in Amyloid Folds: Techniques for Detection and Characterization

Raimon Sabaté and Salvador Ventura

16. Analyzing Oligomerization of Individual Transmembrane Helices and of Entire Membrane Proteins in E. coli: A Hitchhiker´s Guide to GALLEX

Florian Cymer, Charles R. Sanders, and Dirk Schneider

17. Super-secondary Structure Prediction of Transmembrane Beta-Barrel Proteins

Van Du T Tran, Philippe Chassignet and Jean-Marc Steyaert

18. Functional Structural Motifs for Protein-ligand, Protein-protein and Protein-nucleic Acid Interactions and their Connection to Supersecondary Structures

Akira R. Kinjo and Haruki Nakamura

4. Structure Description and Identification using the Tableau Representation of Protein Folding Patterns

Arun S. Konagurthu and Arthur M. Lesk

Part II: Super-secondary Structure Prediction

5. Computational Prediction of Secondary and Supersecondary Structures

Ke Chen and Lukasz Kurgan

6. A Survey of Machine Learning Methods for Secondary and Supersecondary Protein Structure Prediction

Hui Kian Ho, Lei Zhang, Kotagiri Ramamohanarao, and Shawn Martin

7. Beyond Supersecondary Structure: The Global Properties of Protein Sequences

S. Rackovsky

8. Creating Supersecondary Structures with BuildBeta

Silvia Crivelli and Nelson Max

9. A Modular Perspective of P