Protein Supersecondary Structures (2^nd Ed., 2nd ed. 2019)
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1958

This second edition volume expands on the previous edition with an update on the latest developments in the field and new techniques used to study secondary and supersecondary structures (SSS) in proteins. Chapters in this book discuss topics such as sequence and structural features of different SSS elements; software used for the automatic annotation of secondary structure elements in proteins; the new developments in secondary and SSS prediction and the modern approaches for energy landscape calculation; protein misfolding and amyloid structural formation; analysis of ?transformer proteins?; discovery of the structure of the hydrophobic nucleus; and discussions of the main principles of protein structures formation. The contributing authors of the volume are the eminent experts in the field of protein research and bioinformatics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and authoritative, Protein Supersecondary Structures: Methods and Protocols, Second Edition is a valuable resource for researchers who are interested in learning more about  the relationship between amino acids sequences and protein structures, the evolution of proteins and the dynamics of protein formation.

Annotation…

Preface…

Table of Contents…

Contributing Authors…

1. 55 Years of the Rossmann Fold

Woong-Hee Shin and Daisuke Kihara

2. Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction

Elijah MacCarthy, Derrick Perry, and Dukka B. KC

3. Automated Family-Wide Annotation of Secondary Structure Elements

Adam Midlik, Ivana Hutařová Vařeková, Jan Hutař, Taraka Ramji Moturu, Veronika Navrátilová, Jaroslav Koča, Karel Berka, and Radka Svobodová Vařeková

4.    Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences

Christopher J. Oldfield, Ke Chen, and Lukasz Kurgan

5. StackSSSPred: A Stacking Based Prediction of Supersecondary Structure from Sequence

Michael Flot, Avdesh Mishra, Aditi Sharma Kuchi, and Md Tamjidul Hoque

6. Information-Theoretic Inference of an Optimal Dictionary of Protein Supersecondary Structures

Arun S. Konagurthu, Ramanan Subramanian, Lloyd Allison, David Abramson, Maria Garcia de la Banda, Peter J. Stuckey, and Arthur M. Lesk

7. Secondary and Supersecondary Structure of Proteins as Coupling between Local and Local and Backbone-Electrostatic Interactions: A View through Cluster-Cumulant Scope 

Adam Liwo, Adam K. Sieradzan, and Cezary Czaplewski

8. Learning Organizations of Protein Energy Landscapes: An Application on Decoy Selection in Template-Free Protein Structure Prediction

Nasrin Akhter, Liban Hassan, Zahra Rajabi, Daniel Barbará, and Amarda Shehu

9. Exploring Protein Supersecondary Structure through Changes in Protein Folding, Stability, and Flexibility

Douglas E. V. Pires, Carlos H. M. Rodrigues, Amanda T. S. Albanaz, Malancha Karmakar, Yoochan Myung, Joicymara Xavier, Eleni-Maria Michanetzi, Stephanie Portelli, and  David B. Ascher

10. Protodomains: Symmetry Related Supersecondary Structures in Proteins and Self-Complementarity

Philippe Youkharibache

11.  bab Super Secondary Motifs: Sequence, Structural Overview and Pursuit of Potential Autonomously Folding bab Sequences from (b/a)8/TIM Barrels

Rajasekhar Varma Kadamuri, Shivkumar Sharma Irukuvajjula, and Ramakrishna Vadrevu

12.  Formation of Cross-Beta Supersecondary Structure by Soft-Amyloid Cores: Strategies for their Prediction and Characterization

M. Rosario Fernández, Irantzu Pallarès, Valentín Iglesias, Jaime Santos, and Salvador Ventura

13. Stable Sub-Structures in Proteins and How to Find Them using Single-Molecule Force Spectroscopy

Katarzyna Tych and Gabriel Žoldák

14. Supersecondary Structures and Fragment Libraries

Raphael Trevizani and Fábio Lima Custódio

15. Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins

Bernard S. Gerstman, Prem P. Chapagain, Jeevan GC, and Timothy Steckmann

16. Sequence Pattern for Supersecondary Structure of Sandwich-Like Proteins

Alexander Kister

17. Homology Searches using Supersecondary Structure Code

Hiroshi Izumi

18. Beyond Supersecondary Structure: Physics-Based Sequence Alignment

Shalom Rackovsky

19.  Secondary and Supersecondary Structure of Proteins in Light of the Structure of Hydrophobic Cores

Mateusz Banach, Leszek Konieczny, and Irena Roterman

20.  Hands On: Using Tryptophan Fluorescence Spectroscopy to Study Protein Structure

Nadja Hellmann and Dirk Schneider

21. Structural Characterization of Membrane Protein Dimers

António J. Preto, Pedro Matos-Filipe, Panagiotis I. Koukos, Pedro Renault, Sérgio F. Sousa, and Irina S. Moreira