Protein Structure Prediction / Edition 2

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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.

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Product Details

  • ISBN-13: 9781588297525
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 10/28/2007
  • Series: Methods in Molecular Biology Series, #413
  • Edition description: 2nd ed. 2008
  • Edition number: 2
  • Pages: 337
  • Product dimensions: 6.46 (w) x 9.16 (h) x 1.04 (d)

Table of Contents

Preface     v
Contributors     xi
Overview of Protein Structure Prediction
A Historical Perspective of Template-Based Protein Structure Prediction   Jun-tao Guo   Kyle Ellrott   Ying Xu     3
The Assessment of Methods for Protein Structure Prediction   Anna Tramontano   Domenico Cozzetto   Alejandro Giorgetti   Domenico Raimondo     43
Template-based Methods
Aligning Sequences to Structures   Liam James McGuffin     61
Protein Structure Prediction Using Threading   Jinbo Xu   Feng Jiao   Libo Yu     91
Structure Alignment and Indexing
Algorithms for Multiple Protein Structure Alignment and Structure-Derived Multiple Sequence Alignment   Maxim Shatsky   Ruth Nussinov   Haim J. Wolfson     125
Indexing Protein Structures Using Suffix Trees   Feng Gao   Mohammed J. Zaki     147
Protein Features Prediction
Hidden Markov Models for Prediction of Protein Features   Christopher Bystroff   Anders Krogh     173
The Pros and Cons of Predicting Protein Contact Maps   Lisa Bartoli   Emidio Capriotti   Piero Fariselli   Pier Luigi Martelli   Rita Casadio     199
RoadmapMethods for Protein Folding   Mark Moll   David Schwarz   Lydia E. Kavraki     219
Methods for de novo Structure Prediction
Scoring Functions for De Novo Protein Structure Prediction Revisited   Shing-Chung Ngan   Ling-Hong Hung   Tianyun Liu   Ram Samudrala     243
Protein-Protein Docking: Overview and Performance Analysis   Kevin Wiehe   Matthew W. Peterson   Brian Pierce   Julian Mintseris   Zhiping Weng     283
Molecular Dynamics Simulations of Protein Folding   Angel E. Garcia     315
Index     331
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