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Protein Structure Prediction

  • Book
  • © 2008

Overview

Editors:
  1. Mohammed J. Zaki

    1. Rensselaer Polytechnic Institute, Troy, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Christopher Bystroff

    1. Rensselaer Polytechnic Institute, Troy, USA

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    You can also search for this editor in PubMed   Google Scholar

  • Describes cutting-edge techniques for prediction and accesses them from the perspective of their most well-known practitioners
  • Includes a comprehensive account of the history of protein structure prediction
  • Step-by-step, readily reproducible laboratory protocols
  • Chapters written by experienced practitioners

Part of the book series: Methods in Molecular Biology (MIMB, volume 413)

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Table of contents (12 protocols)

  1. Front Matter

    Pages i-xii
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  2. Overview of Protein Structure Prediction

    1. Front Matter

      Pages 1-1
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    2. A Historical Perspective of Template-Based Protein Structure Prediction

      • Jun-tao Guo, Kyle Ellrott, Ying Xu
      Pages 3-42

    3. The Assessment of Methods for Protein Structure Prediction

      • Anna Tramontano, Domenico Cozzetto, Alejandro Giorgetti, Domenico Raimondo
      Pages 43-57

  3. Template-based Methods

    1. Front Matter

      Pages 59-59
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    2. Aligning Sequences to Structures

      • Liam James McGuffin
      Pages 61-90

    3. Protein Structure Prediction Using Threading

      • Jinbo Xu, Feng Jiao, Libo Yu
      Pages 91-121

  4. Structure Alignment and Indexing

    1. Front Matter

      Pages 123-123
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    2. Algorithms for Multiple Protein Structure Alignment and Structure-Derived Multiple Sequence Alignment

      • Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson
      Pages 125-146

    3. Indexing Protein Structures Using Suffix Trees

      • Feng Gao, Mohammed J. Zaki
      Pages 147-169

  5. Protein Features Prediction

    1. Front Matter

      Pages 171-171
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    2. Hidden Markov Models for Prediction of Protein Features

      • Christopher Bystroff, Anders Krogh
      Pages 173-198

    3. The Pros and Cons of Predicting Protein Contact Maps

      • Lisa Bartoli, Emidio Capriotti, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
      Pages 199-217

    4. Roadmap Methods for Protein Folding

      • Mark Moll, David Schwarz, Lydia E. Kavraki
      Pages 219-239

  6. Methods for de novo Structure Prediction

    1. Front Matter

      Pages 241-241
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    2. Scoring Functions for De Novo Protein Structure Prediction Revisited

      • Shing-Chung Ngan, Ling-Hong Hung, Tianyun Liu, Ram Samudrala
      Pages 243-281

    3. Protein–Protein Docking: Overview and Performance Analysis

      • Kevin Wiehe, Matthew W. Peterson, Brian Pierce, Julian Mintseris, Zhiping Weng
      Pages 283-314

    4. Molecular Dynamics Simulations of Protein Folding

      • Angel E. Garcia
      Pages 315-330

  7. Back Matter

    Pages 331-337
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Keywords

About this book

This book covers elements of both the data-driven comparative modeling approach to structure prediction and also recent attempts to simulate folding using explicit or simplified models. Despite the unsolved mystery of how a protein folds, advances are being made in predicting the interactions of proteins with other molecules, such as small ligands, nucleic acids or other proteins. Also rapidly advancing are the methods for solving the inverse folding problem, the problem of finding a sequence to fit a structure. This book focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well known practitioners.

Editors and Affiliations

  • Rensselaer Polytechnic Institute, Troy, USA

    Mohammed J. Zaki, Christopher Bystroff

Bibliographic Information

  • Book Title: Protein Structure Prediction

  • Editors: Mohammed J. Zaki, Christopher Bystroff

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-59745-574-9

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2008

  • Hardcover ISBN: 978-1-58829-752-5Published: 12 September 2007

  • Softcover ISBN: 978-1-61737-757-0Published: 19 November 2010

  • eBook ISBN: 978-1-59745-574-9Published: 03 February 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XII, 337

  • Number of Illustrations: 69 b/w illustrations

  • Topics: Protein Science, Biochemistry, general, Proteomics

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