Protein Supersecondary Structures: Methods and Protocols

Front Matter ....Pages i-xviii
 55 Years of the Rossmann Fold  (Woong-Hee Shin, Daisuke Kihara)....Pages 1-13
 Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction  (Elijah MacCarthy, Derrick Perry, Dukka B. KC)....Pages 15-45
 Automated Family-Wide Annotation of Secondary Structure Elements  (Adam Midlik, Ivana Hutařová Vařeková, Jan Hutař, Taraka Ramji Moturu, Veronika Navrátilová, Jaroslav Koča et al.)....Pages 47-71
 Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences  (Christopher J. Oldfield, Ke Chen, Lukasz Kurgan)....Pages 73-100
 StackSSSPred: A Stacking-Based Prediction of Supersecondary Structure from Sequence  (Michael Flot, Avdesh Mishra, Aditi Sharma Kuchi, Md Tamjidul Hoque)....Pages 101-122
 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 et al.)....Pages 123-131
 Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope  (Adam Liwo, Adam K. Sieradzan, Cezary Czaplewski)....Pages 133-146
 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, Amarda Shehu)....Pages 147-171
 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 et al.)....Pages 173-185
 Protodomains: Symmetry-Related Supersecondary Structures in Proteins and Self-Complementarity  (Philippe Youkharibache)....Pages 187-219
 βαβ Super-Secondary Motifs: Sequence, Structural Overview, and Pursuit of Potential Autonomously Folding βαβ Sequences from (β/α)8/TIM Barrels  (Rajasekhar Varma Kadamuri, Shivkumar Sharma Irukuvajjula, Ramakrishna Vadrevu)....Pages 221-236
 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, Salvador Ventura)....Pages 237-261
 Stable Substructures in Proteins and How to Find Them Using Single-Molecule Force Spectroscopy  (Katarzyna Tych, Gabriel Žoldák)....Pages 263-282
 Supersecondary Structures and Fragment Libraries  (Raphael Trevizani, Fábio Lima Custódio)....Pages 283-295
 Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins  (Bernard S. Gerstman, Prem P. Chapagain, Jeevan GC, Timothy Steckmann)....Pages 297-311
 Sequence Pattern for Supersecondary Structure of Sandwich-Like Proteins  (Alexander E. Kister)....Pages 313-327
 Homology Searches Using Supersecondary Structure Code  (Hiroshi Izumi)....Pages 329-340
 Beyond Supersecondary Structure: Physics-Based Sequence Alignment  (S. Rackovsky)....Pages 341-346
 Secondary and Supersecondary Structure of Proteins in Light of the Structure of Hydrophobic Cores  (Mateusz Banach, Leszek Konieczny, Irena Roterman)....Pages 347-378
 Hands On: Using Tryptophan Fluorescence Spectroscopy to Study Protein Structure  (Nadja Hellmann, Dirk Schneider)....Pages 379-401
 Structural Characterization of Membrane Protein Dimers  (António J. Preto, Pedro Matos-Filipe, Panagiotis I. Koukos, Pedro Renault, Sérgio F. Sousa, Irina S. Moreira)....Pages 403-436
Back Matter ....Pages 437-438