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Protein Structure Prediction

  • Book
  • © 2020

Overview

Editors:
  1. Daisuke Kihara

    1. Department of Computer Science, Purdue University, West Lafayette, USA

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  • 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 2165)

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xii
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  2. Structural Modeling and Ligand-Binding Prediction for Analysis of Structure-Unknown and Function-Unknown Proteins Using FORTE Alignment and PoSSuM Pocket Search

    • Yuko Tsuchiya, Kentaro Tomii
    Pages 1-11

  3. The MULTICOM Protein Structure Prediction Server Empowered by Deep Learning and Contact Distance Prediction

    • Jie Hou, Tianqi Wu, Zhiye Guo, Farhan Quadir, Jianlin Cheng
    Pages 13-26

  4. The Genome3D Consortium for Structural Annotations of Selected Model Organisms

    • Vaishali P. Waman, Tom L. Blundell, Daniel W. A. Buchan, Julian Gough, David Jones, Lawrence Kelley et al.
    Pages 27-67

  5. Estimating the Quality of 3D Protein Models Using the ModFOLD7 Server

    • Ali H. A. Maghrabi, Liam J. McGuffin
    Pages 69-81

  6. Prediction of Intrinsic Disorder with Quality Assessment Using QUARTER

    • Zhonghua Wu, Gang Hu, Christopher J. Oldfield, Lukasz Kurgan
    Pages 83-101

  7. Modeling of Three-Dimensional RNA Structures Using SimRNA

    • Tomasz K. Wirecki, Chandran Nithin, Sunandan Mukherjee, Janusz M. Bujnicki, MichaÅ‚ J. Boniecki
    Pages 103-125

  8. Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server

    • Minkyung Baek, Taeyong Park, Lim Heo, Chaok Seok
    Pages 127-137

  9. Template-Based Modeling of Protein Complexes Using the PPI3D Web Server

    • Justas DapkÅ«nas, ÄŒeslovas Venclovas
    Pages 139-155

  10. Protein–Protein and Protein–Peptide Docking with ClusPro Server

    • Andrey Alekseenko, Mikhail Ignatov, George Jones, Maria Sabitova, Dima Kozakov
    Pages 157-174

  11. Modeling of Protein Complexes and Molecular Assemblies with pyDock

    • Mireia Rosell, Luis Angel Rodríguez-Lumbreras, Juan Fernández-Recio
    Pages 175-198

  12. A Guide for Protein–Protein Docking Using SwarmDock

    • Iain H. Moal, Raphael A. G. Chaleil, Mieczyslaw Torchala, Paul A. Bates
    Pages 199-216

  13. Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK Webserver

    • Yumeng Yan, Sheng-You Huang
    Pages 217-229

  14. IDP-LZerD: Software for Modeling Disordered Protein Interactions

    • Charles Christoffer, Daisuke Kihara
    Pages 231-244

  15. AnAnaS: Software for Analytical Analysis of Symmetries in Protein Structures

    • Guillaume Pagès, Sergei Grudinin
    Pages 245-257

  16. MDockPeP: A Web Server for Blind Prediction of Protein–Peptide Complex Structures

    • Xianjin Xu, Xiaoqin Zou
    Pages 259-272

  17. Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures

    • Aleksandra E. Badaczewska-Dawid, Alisa Khramushin, Andrzej Kolinski, Ora Schueler-Furman, Sebastian Kmiecik
    Pages 273-287

  18. Dockground Tool for Development and Benchmarking of Protein Docking Procedures

    • Petras J. Kundrotas, Ian Kotthoff, Sherman W. Choi, Matthew M. Copeland, Ilya A. Vakser
    Pages 289-300

  19. Molecular Dynamics Flexible Fitting: All You Want to Know About Resolution Exchange

    • John W. Vant, Daipayan Sarkar, Chitrak Gupta, Mrinal S. Shekhar, Sumit Mittal, Abhishek Singharoy
    Pages 301-315

  20. Protein Structure Modeling from Cryo-EM Map Using MAINMAST and MAINMAST-GUI Plugin

    • Genki Terashi, Yuhong Zha, Daisuke Kihara
    Pages 317-336
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Keywords

About this book

This thorough new edition explores web servers and software for protein structure prediction and modeling that are freely available to the academic community. Taking into account the numerous advances in the computational protein structure prediction/modeling field, the book includes residue-contact prediction via deep learning, a wide variety of protein docking models, as well as cryo-electron microscopy (cryo-EM) techniques. Written by renowned experts in the field and for the highly successful Methods in Molecular Biology series, chapters include the kind of key detail and implementation advice necessary for researchers to achieve optimal results in their own work. 

Authoritative and fully updated, Protein Structure Prediction, Fourth Edition is a practical and immediately useful guide for biology researchers working toward modeling protein structures.
































Editors and Affiliations

  • Department of Computer Science, Purdue University, West Lafayette, USA

    Daisuke Kihara

Bibliographic Information

  • Book Title: Protein Structure Prediction

  • Editors: Daisuke Kihara

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0708-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

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

  • Hardcover ISBN: 978-1-0716-0707-7Published: 04 July 2020

  • Softcover ISBN: 978-1-0716-0710-7Published: 05 July 2021

  • eBook ISBN: 978-1-0716-0708-4Published: 03 July 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 4

  • Number of Pages: XII, 358

  • Number of Illustrations: 8 b/w illustrations, 108 illustrations in colour

  • Topics: Protein Science, Bioinformatics, Chemistry/Food Science, general

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