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Protein Structure Prediction

  • Book
  • © 2014

Overview

Editors:
  1. Daisuke Kihara

    1. Purdue University Dept. Biological Science, West Lafayette, USA

    View editor publications

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  • Details the expansion of the computational protein structure prediction field
  • 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 1137)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Protein Structure Modeling with MODELLER

    • Benjamin Webb, Andrej Sali
    Pages 1-15

  3. RaptorX server: A Resource for Template-Based Protein Structure Modeling

    • Morten Källberg, Gohar Margaryan, Sheng Wang, Jianzhu Ma, Jinbo Xu
    Pages 17-27

  4. The MULTICOM Protein Tertiary Structure Prediction System

    • Jilong Li, Debswapna Bhattacharya, Renzhi Cao, Badri Adhikari, Xin Deng, Jesse Eickholt et al.
    Pages 29-41

  5. Modeling of Protein Side-Chain Conformations with RASP

    • Zhichao Miao, Yang Cao, Taijiao Jiang
    Pages 43-53

  6. Direct Coupling Analysis for Protein Contact Prediction

    • Faruck Morcos, Terence Hwa, José N. Onuchic, Martin Weigt
    Pages 55-70

  7. ITScorePro: An Efficient Scoring Program for Evaluating the Energy Scores of Protein Structures for Structure Prediction

    • Sheng-You Huang, Xiaoqin Zou
    Pages 71-81

  8. Assessing the Quality of Modelled 3D Protein Structures Using the ModFOLD Server

    • Daniel Barry Roche, Maria Teresa Buenavista, Liam James McGuffin
    Pages 83-103

  9. 3D-SURFER 2.0: Web Platform for Real-Time Search and Characterization of Protein Surfaces

    • Yi Xiong, Juan Esquivel-Rodriguez, Lee Sael, Daisuke Kihara
    Pages 105-117

  10. SPOT-Seq-RNA: Predicting Protein–RNA Complex Structure and RNA-Binding Function by Fold Recognition and Binding Affinity Prediction

    • Yuedong Yang, Huiying Zhao, Jihua Wang, Yaoqi Zhou
    Pages 119-130

  11. POODLE: Tools Predicting Intrinsically Disordered Regions of Amino Acid Sequence

    • Kana Shimizu
    Pages 131-145

  12. Prediction of Intrinsic Disorder in Proteins Using MFDp2

    • Marcin J. Mizianty, Vladimir Uversky, Lukasz Kurgan
    Pages 147-162

  13. Modeling Protein–Protein Complexes Using the HADDOCK Webserver “Modeling Protein Complexes with HADDOCK”

    • Gydo C. P. van Zundert, Alexandre M. J. J. Bonvin
    Pages 163-179

  14. Predicting the Structure of Protein–Protein Complexes Using the SwarmDock Web Server

    • Mieczyslaw Torchala, Paul A. Bates
    Pages 181-197

  15. DOCK/PIERR: Web Server for Structure Prediction of Protein–Protein Complexes

    • Shruthi Viswanath, D. V. S. Ravikant, Ron Elber
    Pages 199-207

  16. Pairwise and Multimeric Protein–Protein Docking Using the LZerD Program Suite

    • Juan Esquivel-Rodriguez, Vianney Filos-Gonzalez, Bin Li, Daisuke Kihara
    Pages 209-234

  17. Protocols for Efficient Simulations of Long-Time Protein Dynamics Using Coarse-Grained CABS Model

    • Michal Jamroz, Andrzej Kolinski, Sebastian Kmiecik
    Pages 235-250

  18. Back Matter

    Pages 251-253
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Keywords

About this book

Protein Structure Prediction, Third Edition expands on previous editions by focusing on software and web servers. With new chapters that provide instructions on how to use a computational method with examples of prediction by the method. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Protein Structure Prediction, Third Edition provides diverse methods detailing the expansion of the computational protein structure prediction field.

Editors and Affiliations

  • Purdue University Dept. Biological Science, 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/10.1007/978-1-4939-0366-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2014

  • Hardcover ISBN: 978-1-4939-0365-8Published: 27 February 2014

  • Softcover ISBN: 978-1-4939-4461-3Published: 23 August 2016

  • eBook ISBN: 978-1-4939-0366-5Published: 08 July 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 3

  • Number of Pages: XI, 253

  • Number of Illustrations: 16 b/w illustrations, 48 illustrations in colour

  • Topics: Protein Science, Protein Structure

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