Homology Modeling: Methods and Protocols

ISBN-13: 9781071629734 / Angielski / Twarda / 2023 / 444 str.

Slawomir Filipek

Opis

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.

Spis treści

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

            Rym Ben Boubaker, Asma Tiss, Daniel Henrion, and Marie Chabbert

 

2. Illuminating the ‘Twilight Zone’: Advances in Difficult Protein Modeling

            Damian Bartuzi, Agnieszka A. Kaczor, and Dariusz Matosiuk

 

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

            Sutanu Bhattacharya, Rahmatullah Roche, Md Hossain Shuvo, Bernard Moussad, and Debswapna Bhattacharya

 

4. Omics and Remote Homology Integration to Decipher Protein Functionality

            Liliana Silva and Agostinho Antunes

 

5. Easy not Easy: Comparative Modeling with High Sequence Identity Templates

            Diego Javier Zea, Elin Teppa, and Cristina Marino-Buslje

 

6. Quality Estimates for 3D Protein Models

            Ali H.A. Maghrabi, Fahd M.F. Aldowsari, and Liam J. McGuffin

 

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

            Recep Adiyaman and Liam J. McGuffin

 

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

            Julia Koehler Leman and Richard Bonneau

 

9. Homology Modeling of the G Protein-Coupled Receptors

            Stefan Mordalski and Tomasz Kościółek

 

10. Modeling of Olfactory Receptors

            Xueying Wang, H.C. Stephen Chan, and Shuguang Yuan

 

11. Analyses of Mutation Displacements from Homology Models

            Mathilde Carpentier and Jacques Chomilier

 

12. Persistent Homology for RNA Data Analysis

            Kelin Xia, Xiang Liu, and JunJie Wee

 

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

            Hiroto Anbo, Motonori Ota, and Satoshi Fukuchi

 

14. Homology Modeling of Transporter Proteins

            Ingebrigt Sylte, Mari Gabrielsen, and Kurt Kristiansen

 

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

            Manish Sarkar and Soham Saha

 

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

            Harsh Bansia and Suryanarayanarao Ramakumar

 

17. 3D-BMPP: 3D Beta-Barrel Membrane Protein Predictor

            Wei Tian, Meishan Lin, Ke Tang, Manisha Barse, Hammad Naveed, and Jie Liang

 

18. Protein Homology Modeling for Effective Drug Design

            Natalia Gniado, Agata Krawczyk-Balska, Pakhuri Mehta, Przemysław Miszta, and Sławomir Filipek

 

19. Specificities of Protein Homology Modeling for Allosteric Drug Design

            Jakub Jakowiecki, Urszula Orzeł, Aleksandra Gliździnska, Mariusz Możajew, and Sławomir Filipek

 

20. Modeling of Protein Complexes

            Luigi Scietti and Federico Forneris