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Structural Bioinformatics

Methods and Protocols

  • Book
  • © 2020

Overview

Editors:
  1. Zoltán Gáspári

    1. Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary

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    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2112)

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About this book

This volume looks at the latest techniques used to perform comparative structure analyses, and predict and evaluate protein-ligand interactions. The chapters in this book cover tools and servers such as LiteMol; Bio3D-Web; DALI; CATH; HoTMuSiC, a contact-base protein structure analysis tool known as CAD-Score; PyDockSaxs and HADDOCK; CombDock and DockStar; the BioMagResBank database; as well as BME and CoNSEnsX+. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls.


Cutting-edge and comprehensive, Structural Bioinformatics: Methods and Protocols is a practical guide for researchers to learn more about the aforementioned tools to further enhance their studies in the growing field of structural bioinformatics.


Chapter 13 isavailable open access under a CC-BY 4.0 license via link.springer.com.



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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xii
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  2. Visualization and Analysis of Protein Structures with LiteMol Suite

    • David Sehnal, Radka Svobodová, Karel Berka, Lukáš Pravda, Adam Midlik, Jaroslav Koča
    Pages 1-13

  3. Comparative Protein Structure Analysis with Bio3D-Web

    • Barry J. Grant, Lars Skjærven, Xin-Qiu Yao
    Pages 15-28

  4. Using Dali for Protein Structure Comparison

    • Liisa Holm
    Pages 29-42

  5. Assessing Protein Function Through Structural Similarities with CATH

    • Natalie L. Dawson, Christine Orengo, Zoltán Gáspári
    Pages 43-57

  6. Protein Thermal Stability Engineering Using HoTMuSiC

    • Fabrizio Pucci, Jean Marc Kwasigroch, Marianne Rooman
    Pages 59-73

  7. Contact Area-Based Structural Analysis of Proteins and Their Complexes Using CAD-Score

    • Kliment Olechnovič, Česlovas Venclovas
    Pages 75-90

  8. A Comprehensive Computational Platform to Guide Drug Development Using Graph-Based Signature Methods

    • Douglas E. V. Pires, Stephanie Portelli, Pâmela M. Rezende, Wandré N. P. Veloso, Joicymara S. Xavier, Malancha Karmakar et al.
    Pages 91-106

  9. Systematic Exploration of Binding Modes of Ligands on Drug Targets

    • Csaba Hetényi, Mónika Bálint
    Pages 107-121

  10. Using MemBlob to Analyze Transmembrane Regions Based on Cryo-EM Maps

    • Georgina Csizmadia, Bianka Farkas, Eszter Katona, Gábor E. Tusnády, Tamás Hegedűs
    Pages 123-130

  11. Structural Characterization of Protein–Protein Interactions with pyDockSAXS

    • Brian Jiménez-García, Pau Bernadó, Juan Fernández-Recio
    Pages 131-144

  12. Protein–Protein Modeling Using Cryo-EM Restraints

    • Mikael Trellet, Gydo van Zundert, Alexandre M. J. J. Bonvin
    Pages 145-162

  13. Modeling of Multimolecular Complexes

    • Dina Schneidman-Duhovny, Haim J. Wolfson
    Pages 163-174

  14. Biological Assembly Comparison with VAST+

    • Thomas Madej, Aron Marchler-Bauer, Christopher Lanczycki, Dachuan Zhang, Stephen H. Bryant
    Pages 175-186Open Access

  15. BioMagResBank (BMRB) as a Resource for Structural Biology

    • Pedro R. Romero, Naohiro Kobayashi, Jonathan R. Wedell, Kumaran Baskaran, Takeshi Iwata, Masashi Yokochi et al.
    Pages 187-218

  16. Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach

    • Sandro Bottaro, Tone Bengtsen, Kresten Lindorff-Larsen
    Pages 219-240

  17. Evaluation and Selection of Dynamic Protein Structural Ensembles with CoNSEnsX+

    • Dániel Dudola, Bertalan Kovács, Zoltán Gáspári
    Pages 241-254

  18. Back Matter

    Pages 255-256
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Editors and Affiliations

  • Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary

    Zoltán Gáspári

Bibliographic Information

  • Book Title: Structural Bioinformatics

  • Book Subtitle: Methods and Protocols

  • Editors: Zoltán Gáspári

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0270-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2020

  • Hardcover ISBN: 978-1-0716-0269-0Published: 01 February 2020

  • Softcover ISBN: 978-1-0716-0272-0Published: 01 February 2021

  • eBook ISBN: 978-1-0716-0270-6Published: 31 January 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 256

  • Number of Illustrations: 10 b/w illustrations, 76 illustrations in colour

  • Topics: Bioinformatics

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