Homology Modeling

Methods and Protocols

Editors:

ISBN: 978-1-61779-587-9 (Print) 978-1-61779-588-6 (Online)

Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi

  2. No Access

    Book Protocol

    Pages 1-31

    Classification of Proteins: Available Structural Space for Molecular Modeling

  3. No Access

    Book Protocol

    Pages 33-54

    Effective Techniques for Protein Structure Mining

  4. No Access

    Book Protocol

    Pages 55-82

    Methods for Sequence–Structure Alignment

  5. No Access

    Book Protocol

    Pages 83-106

    Force Fields for Homology Modeling

  6. No Access

    Book Protocol

    Pages 107-136

    Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal

  7. No Access

    Book Protocol

    Pages 137-173

    A Practical Introduction to Molecular Dynamics Simulations: Applications to Homology Modeling

  8. No Access

    Book Protocol

    Pages 175-188

    Methods for Accurate Homology Modeling by Global Optimization

  9. No Access

    Book Protocol

    Pages 189-205

    Ligand-Guided Receptor Optimization

  10. No Access

    Book Protocol

    Pages 207-229

    Loop Simulations

  11. No Access

    Book Protocol

    Pages 231-257

    Methods of Protein Structure Comparison

  12. No Access

    Book Protocol

    Pages 259-279

    Homology Modeling of Class A G Protein-Coupled Receptors

  13. No Access

    Book Protocol

    Pages 281-299

    Homology Modeling of Transporter Proteins (Carriers and Ion Channels)

  14. No Access

    Book Protocol

    Pages 301-311

    Methods for the Homology Modeling of Antibody Variable Regions

  15. No Access

    Book Protocol

    Pages 313-330

    Investigating Protein Variants Using Structural Calculation Techniques

  16. No Access

    Book Protocol

    Pages 331-350

    Macromolecular Assembly Structures by Comparative Modeling and Electron Microscopy

  17. No Access

    Book Protocol

    Pages 351-373

    Preparation and Refinement of Model Protein–Ligand Complexes

  18. No Access

    Book Protocol

    Pages 375-398

    Modeling Peptide–Protein Interactions

  19. No Access

    Book Protocol

    Pages 399-414

    Comparison of Common Homology Modeling Algorithms: Application of User-Defined Alignments

  20. Back Matter

    Pages 415-419