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Protein Supersecondary Structures

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Alexander E. Kister

    1. Department of Mathematics, Rutgers University, Piscataway, USA

    View editor publications

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1958)

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xviii
    Download chapter PDF

  2. 55 Years of the Rossmann Fold

    • Woong-Hee Shin, Daisuke Kihara
    Pages 1-13

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

    • Elijah MacCarthy, Derrick Perry, Dukka B. KC
    Pages 15-45

  4. 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

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

    • Christopher J. Oldfield, Ke Chen, Lukasz Kurgan
    Pages 73-100

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

    • Michael Flot, Avdesh Mishra, Aditi Sharma Kuchi, Md Tamjidul Hoque
    Pages 101-122

  7. 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

  8. 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

  9. 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

  10. 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

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

    • Philippe Youkharibache
    Pages 187-219

  12. 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

  13. 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

  14. Stable Substructures in Proteins and How to Find Them Using Single-Molecule Force Spectroscopy

    • Katarzyna Tych, Gabriel Žoldák
    Pages 263-282

  15. Supersecondary Structures and Fragment Libraries

    • Raphael Trevizani, Fábio Lima Custódio
    Pages 283-295

  16. Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins

    • Bernard S. Gerstman, Prem P. Chapagain, Jeevan GC, Timothy Steckmann
    Pages 297-311

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

    • Alexander E. Kister
    Pages 313-327

  18. Homology Searches Using Supersecondary Structure Code

    • Hiroshi Izumi
    Pages 329-340

  19. Beyond Supersecondary Structure: Physics-Based Sequence Alignment

    • S. Rackovsky
    Pages 341-346

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

    • Mateusz Banach, Leszek Konieczny, Irena Roterman
    Pages 347-378
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Keywords

About this book

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 ofthe 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.




Editors and Affiliations

  • Department of Mathematics, Rutgers University, Piscataway, USA

    Alexander E. Kister

Bibliographic Information

  • Book Title: Protein Supersecondary Structures

  • Book Subtitle: Methods and Protocols

  • Editors: Alexander E. Kister

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9161-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9160-0Published: 04 April 2019

  • eBook ISBN: 978-1-4939-9161-7Published: 03 April 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XVIII, 438

  • Number of Illustrations: 16 b/w illustrations, 103 illustrations in colour

  • Topics: Protein Structure, Bioinformatics

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