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
Soren 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 Munoz
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 Sabate and Salvador Ventura
16. Analyzing Oligomerization of Individual Transmembrane Helices and of Entire Membrane Proteins in E. coli: A Hitchhikers 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 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 Munoz
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 Sabate and Salvador Ventura
16. Analyzing Oligomerization of Individual Transmembrane Helices and of Entire Membrane Proteins in E. coli: A Hitchhikers 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
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 Munoz
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 Sabate and Salvador Ventura
16. Analyzing Oligomerization of Individual Transmembrane Helices and of Entire Membrane Proteins in E. coli: A Hitchhikers 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
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 Sabate and Salvador Ventura
16. Analyzing Oligomerization of Individual Transmembrane Helices and of Entire Membrane Proteins in E. coli: A Hitchhikers 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
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
