Protein Supersecondary Structures: Methods and Protocols (Hardcover, 2, 2019)

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 Hutarova Varekova, Jan Hutar, Taraka Ramji Moturu, Veronika Navratilova, Jaroslav Koca, Karel Berka, and Radka Svobodova Varekova 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 Barbara, 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 Fernandez, Irantzu Pallares, Valentin 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 Zoldak 14. Supersecondary Structures and Fragment Libraries Raphael Trevizani and Fabio Lima Custodio 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 Antonio J. Preto, Pedro Matos-Filipe, Panagiotis I. Koukos, Pedro Renault, Sergio F. Sousa, and Irina S. Moreira