Skip to main content
SpringerLink
Log in

Homology Modeling

Methods and Protocols

  • Book
  • © 2023

Overview

Editors:
  1. Sławomir Filipek

    1. Faculty of Chemistry, University of Warsaw, Warsaw, Poland

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2627)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

Table of contents (20 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Homology Modeling in the Twilight Zone: Improved Accuracy by Sequence Space Analysis

    • Rym Ben Boubaker, Asma Tiss, Daniel Henrion, Marie Chabbert
    Pages 1-23

  3. Illuminating the “Twilight Zone”: Advances in Difficult Protein Modeling

    • Damian Bartuzi, Agnieszka A. Kaczor, Dariusz Matosiuk
    Pages 25-40

  4. Contact-Assisted Threading in Low-Homology Protein Modeling

    • Sutanu Bhattacharya, Rahmatullah Roche, Md Hossain Shuvo, Bernard Moussad, Debswapna Bhattacharya
    Pages 41-59

  5. Omics and Remote Homology Integration to Decipher Protein Functionality

    • Liliana Silva, Agostinho Antunes
    Pages 61-81

  6. Easy Not Easy: Comparative Modeling with High-Sequence Identity Templates

    • Diego Javier Zea, Elin Teppa, Cristina Marino-Buslje
    Pages 83-100

  7. Quality Estimates for 3D Protein Models

    • Ali H. A. Maghrabi, Fahd M. F. Aldowsari, Liam J. McGuffin
    Pages 101-118

  8. Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy

    • Recep Adiyaman, Liam J. McGuffin
    Pages 119-140

  9. Specificities of Modeling of Membrane Proteins Using Multi-Template Homology Modeling

    • Julia Koehler Leman, Richard Bonneau
    Pages 141-166

  10. Homology Modeling of the G Protein-Coupled Receptors

    • Stefan Mordalski, Tomasz Kościółek
    Pages 167-181

  11. Modeling of Olfactory Receptors

    • Xueying Wang, H. C. Stephen Chan, Shuguang Yuan
    Pages 183-193

  12. Analyses of Mutation Displacements from Homology Models

    • Mathilde Carpentier, Jacques Chomilier
    Pages 195-210

  13. Persistent Homology for RNA Data Analysis

    • Kelin Xia, Xiang Liu, JunJie Wee
    Pages 211-229

  14. Computational Methods to Predict Intrinsically Disordered Regions and Functional Regions in Them

    • Hiroto Anbo, Motonori Ota, Satoshi Fukuchi
    Pages 231-245

  15. Homology Modeling of Transporter Proteins

    • Ingebrigt Sylte, Mari Gabrielsen, Kurt Kristiansen
    Pages 247-264

  16. Modeling of SARS-CoV-2 Virus Proteins: Implications on Its Proteome

    • Manish Sarkar, Soham Saha
    Pages 265-299

  17. Homology Modeling of Antibody Variable Regions: Methods and Applications

    • Harsh Bansia, Suryanarayanarao Ramakumar
    Pages 301-319

  18. 3D-BMPP: 3D Beta-Barrel Membrane Protein Predictor

    • Wei Tian, Meishan Lin, Ke Tang, Manisha Barse, Hammad Naveed, Jie Liang
    Pages 321-328

  19. Protein Homology Modeling for Effective Drug Design

    • Natalia Gniado, Agata Krawczyk-Balska, Pakhuri Mehta, Przemysław Miszta, Sławomir Filipek
    Pages 329-337

  20. Specificities of Protein Homology Modeling for Allosteric Drug Design

    • Jakub Jakowiecki, Urszula Orzeł, Aleksandra Gliździnska, Mariusz Możajew, Sławomir Filipek
    Pages 339-348
Back to top

Keywords

About this book

This detailed volume provides state-of-the-art methodologies and reviews of important topics in the field of homology modeling. From homology modeling in the twilight zone and improving accuracy through sequence space analysis to approaches to construct multi-protein complex models, the book explores a wide variety of uses and applications of this valuable technique. Written for the highly successful Methods in Molecular Biology series, the chapters include introductions to their respective topics, lists of the necessary programs, webservers, and databases, step-by-step and readily reproducible protocols, as well as tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Homology Modeling: Methods and Protocols serves as an ideal guide to recent homology modeling procedures, assumptions made, and model quality assessment that will illuminate the black box of homology modeling for novice readers and broaden the knowledge of this methodology for professionals.

Editors and Affiliations

  • Faculty of Chemistry, University of Warsaw, Warsaw, Poland

    Sławomir Filipek

Bibliographic Information

  • Book Title: Homology Modeling

  • Book Subtitle: Methods and Protocols

  • Editors: Sławomir Filipek

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2974-1

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2973-4Published: 24 March 2023

  • Softcover ISBN: 978-1-0716-2976-5Published: 24 March 2023

  • eBook ISBN: 978-1-0716-2974-1Published: 23 March 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 376

  • Number of Illustrations: 5 b/w illustrations, 87 illustrations in colour

  • Topics: Bioinformatics, Chemistry/Food Science, general, Biotechnology, Biomaterials

Publish with us

Policies and ethics

Back to top

Search

Navigation