Protein Structure Prediction

  • Mohammed J. Zaki
  • Christopher Bystroff

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

Table of contents

  1. Front Matter
    Pages i-xii
  2. Overview of Protein Structure Prediction

    1. Front Matter
      Pages 1-1
    2. Jun-tao Guo, Kyle Ellrott, Ying Xu
      Pages 3-42
    3. Anna Tramontano, Domenico Cozzetto, Alejandro Giorgetti, Domenico Raimondo
      Pages 43-57
  3. Template-based Methods

    1. Front Matter
      Pages 59-59
    2. Liam James McGuffin
      Pages 61-90
    3. Jinbo Xu, Feng Jiao, Libo Yu
      Pages 91-121
  4. Structure Alignment and Indexing

    1. Front Matter
      Pages 123-123
    2. Feng Gao, Mohammed J. Zaki
      Pages 147-169
  5. Protein Features Prediction

    1. Front Matter
      Pages 171-171
    2. Christopher Bystroff, Anders Krogh
      Pages 173-198
    3. Lisa Bartoli, Emidio Capriotti, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
      Pages 199-217
    4. Mark Moll, David Schwarz, Lydia E. Kavraki
      Pages 219-239
  6. Methods for de novo Structure Prediction

    1. Front Matter
      Pages 241-241
    2. Shing-Chung Ngan, Ling-Hong Hung, Tianyun Liu, Ram Samudrala
      Pages 243-281
    3. Kevin Wiehe, Matthew W. Peterson, Brian Pierce, Julian Mintseris, Zhiping Weng
      Pages 283-314
  7. Back Matter
    Pages 331-337

About this book


For forty years we have known the essential ingredients for protein folding – an amino acid sequence, and water. But the problem of predicting the three-dimensional structure from its sequence has eluded computational biologists even in the age of supercomputers and high throughput structural genomics. 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. Protein Structure Prediction focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well-known practitioners. Leaders in the field provide insights into template-based methods of prediction, structure alignment and indexing, protein features prediction, and methods for de novo structure prediction. Protein Structure Prediction is a cutting-edge text that all researchers in the field should have in their libraries.


Computational methods Data-driven comparative modeling Protein folding Protein interaction Structure alignment protein contact map protein structure protein structure prediction proteins

Editors and affiliations

  • Mohammed J. Zaki
    • 1
  • Christopher Bystroff
    • 1
  1. 1.Rensselaer Polytechnic InstituteTroyUSA

Bibliographic information

  • DOI
  • Copyright Information Humana Press 2008
  • Publisher Name Humana Press
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-58829-752-5
  • Online ISBN 978-1-59745-574-9
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site