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Homology Modeling

Methods and Protocols

  • Book
  • © 2012

Overview

Editors:
  1. Andrew J. W. Orry

    1. Molsoft L.L.C., S209 San Diego, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Ruben Abagyan

    1. Skaggs School of Pharmacy &, Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Describes homology modeling steps from first principles
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 857)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Classification of Proteins: Available Structural Space for Molecular Modeling

    • Antonina Andreeva
    Pages 1-31

  3. Effective Techniques for Protein Structure Mining

    • Stefan J. Suhrer, Markus Gruber, Markus Wiederstein, Manfred J. Sippl
    Pages 33-54

  4. Methods for Sequence–Structure Alignment

    • Česlovas Venclovas
    Pages 55-82

  5. Force Fields for Homology Modeling

    • Andrew J. Bordner
    Pages 83-106

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

    • Lorenza Bordoli, Torsten Schwede
    Pages 107-136

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

    • Alessandra Nurisso, Antoine Daina, Ross C. Walker
    Pages 137-173

  8. Methods for Accurate Homology Modeling by Global Optimization

    • Keehyoung Joo, Jinwoo Lee, Jooyoung Lee
    Pages 175-188

  9. Ligand-Guided Receptor Optimization

    • Vsevolod Katritch, Manuel Rueda, Ruben Abagyan
    Pages 189-205

  10. Loop Simulations

    • Maxim Totrov
    Pages 207-229

  11. Methods of Protein Structure Comparison

    • Irina Kufareva, Ruben Abagyan
    Pages 231-257

  12. Homology Modeling of Class A G Protein-Coupled Receptors

    • Stefano Costanzi
    Pages 259-279

  13. Homology Modeling of Transporter Proteins (Carriers and Ion Channels)

    • Aina Westrheim Ravna, Ingebrigt Sylte
    Pages 281-299

  14. Methods for the Homology Modeling of Antibody Variable Regions

    • Aroop Sircar
    Pages 301-311

  15. Investigating Protein Variants Using Structural Calculation Techniques

    • Jonas Carlsson, Bengt Persson
    Pages 313-330

  16. Macromolecular Assembly Structures by Comparative Modeling and Electron Microscopy

    • Keren Lasker, Javier A. Velázquez-Muriel, Benjamin M. Webb, Zheng Yang, Thomas E. Ferrin, Andrej Sali
    Pages 331-350

  17. Preparation and Refinement of Model Protein–Ligand Complexes

    • Andrew J. W. Orry, Ruben Abagyan
    Pages 351-373

  18. Modeling Peptide–Protein Interactions

    • Nir London, Barak Raveh, Ora Schueler-Furman
    Pages 375-398

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

    • Michael A. Dolan, James W. Noah, Darrell Hurt
    Pages 399-414

  20. Back Matter

    Pages 415-419
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Keywords

About this book

Knowledge about protein tertiary structure can guide experiments, assist in the understanding of structure-function relationships, and aid the design of new therapeutics for disease. Homology modeling is an in silico method that predicts the tertiary structure of an amino acid sequence based on a homologous experimentally determined structure.  In, Homology Modelling: Methods and Protocols experts in the field describe each homology modeling step from first principles, provide case studies for challenging modeling targets and describe methods for the prediction of how other molecules such as drugs can interact with the protein. Written in the highly successful Methods in Molecular Biology™ series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory.

 

Thorough and intuitive, Homology Modelling: Methods and Protocols guides scientists in the available homology modeling methods.

 

Editors and Affiliations

  • Molsoft L.L.C., S209 San Diego, USA

    Andrew J. W. Orry

  • Skaggs School of Pharmacy &, Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA

    Ruben Abagyan

Bibliographic Information

  • Book Title: Homology Modeling

  • Book Subtitle: Methods and Protocols

  • Editors: Andrew J. W. Orry, Ruben Abagyan

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-61779-588-6

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media,LLC 2012

  • Hardcover ISBN: 978-1-61779-587-9Published: 10 February 2012

  • Softcover ISBN: 978-1-4939-5880-1Published: 23 August 2016

  • eBook ISBN: 978-1-61779-588-6Published: 10 February 2012

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 419

  • Number of Illustrations: 34 b/w illustrations, 55 illustrations in colour

  • Topics: Protein Science, Protein Structure

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