Book Volume 932 2013

Protein Supersecondary Structures

Editors:

ISBN: 978-1-62703-064-9 (Print) 978-1-62703-065-6 (Online)

Table of contents (18 protocols)

  1. Front Matter

    Pages i-xvii

  2. No Access

    Protocol

    Pages 1-4

    Super-secondary Structure: A Historical Perspective

  3. Representation of Supersecondary Structure

    1. Front Matter

      Pages 5-5

    2. No Access

      Protocol

      Pages 7-33

      Hierarchical Representation of Supersecondary Structures Using a Graph-Theoretical Approach

    3. No Access

      Protocol

      Pages 35-50

      Up, Down, and Around: Identifying Recurrent Interactions Within and Between Super-secondary Structures in β-Propellers

    4. No Access

      Protocol

      Pages 51-59

      Structure Description and Identification Using the Tableau Representation of Protein Folding Patterns

  4. Super-secondary Structure Prediction

    1. Front Matter

      Pages 61-61

    2. No Access

      Protocol

      Pages 63-86

      Computational Prediction of Secondary and Supersecondary Structures

    3. No Access

      Protocol

      Pages 87-106

      A Survey of Machine Learning Methods for Secondary and Supersecondary Protein Structure Prediction

    4. No Access

      Protocol

      Pages 107-114

      Beyond Supersecondary Structure: The Global Properties of Protein Sequences

    5. No Access

      Protocol

      Pages 115-140

      Creating Supersecondary Structures with BuildBeta

    6. No Access

      Protocol

      Pages 141-158

      A Modular Perspective of Protein Structures: Application to Fragment Based Loop Modeling

    7. No Access

      Protocol

      Pages 159-173

      Residue–Residue Contacts: Application to Analysis of Secondary Structure Interactions

  5. Supersecondary Structure and Protein Folding

    1. Front Matter

      Pages 175-175

    2. No Access

      Protocol

      Pages 177-189

      Super-secondary Structures and Modeling of Protein Folds

    3. No Access

      Protocol

      Pages 191-204

      Computational Simulations of Protein Folding to Engineer Amino Acid Sequences to Encourage Desired Supersecondary Structure Formation

    4. No Access

      Protocol

      Pages 205-218

      Protein Folding at Atomic Resolution: Analysis of Autonomously Folding Supersecondary Structure Motifs by Nuclear Magnetic Resonance

    5. No Access

      Protocol

      Pages 219-234

      Artificial Supersecondary Structures Based on Aromatic Oligoamides

  6. Other Applications of Supersecondary Structure to Protein Biology

    1. Front Matter

      Pages 235-235

    2. No Access

      Protocol

      Pages 237-257

      Cross-β-Sheet Supersecondary Structure in Amyloid Folds: Techniques for Detection and Characterization

    3. No Access

      Protocol

      Pages 259-276

      Analyzing Oligomerization of Individual Transmembrane Helices and of Entire Membrane Proteins in E. coli: A Hitchhiker’s Guide to GALLEX

    4. No Access

      Protocol

      Pages 277-294

      Supersecondary Structure Prediction of Transmembrane Beta-Barrel Proteins

    5. No Access

      Protocol

      Pages 295-315

      Functional Structural Motifs for Protein–Ligand, Protein–Protein, and Protein–Nucleic Acid Interactions and their Connection to Supersecondary Structures

  7. Back Matter

    Pages 317-320