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| New Book Announcement: Protein Structure Predictio |
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[ 2007-10-4 0:11:00 | By: Byron ] |
PROTEIN STRUCTURE PREDICTION
Springer/Humana Press, 2007
ISBN: 978-1-58829-752-5
http://www.cs.rpi.edu/~zaki/prot-book/
EDITED BY
Mohammed J. Zaki, Chris Bystroff
Rensselaer Polytechnic Institute
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.
FEATURES
* Describes cutting-edge approaches for protein structure prediction
* Provides a comprehensive view of structure prediction methods and
their assessment, including template-based approaches, structure
alignment and indexing, feature prediction, and de novo methods
* Chapters written by the most well-known practitioners in their areas
TABLE OF CONTENTS
Overview of Protein Structure Prediction
1. A historical perspective of template-based protein structure
prediction, Jun-tao Guo, Kyle Ellrott, and Ying Xu
2. The assessment of methods for protein structure prediction,
Anna Tramontano, Domenico Cozzetto, Alejandro Giorgetti, and
Domenico Raimondo
Template-based Methods
3. Aligning Sequences to Structures, Liam J. McGuffin
4. Protein Structure Prediction Using Threading
Jinbo Xu, Feng Jiao, and Libo Yu
Structure Alignment and Indexing
5. Algorithms for Multiple Protein Structure Alignment and
Structure-Derived Multiple Sequence Alignment,
Maxim Shatsky, Ruth Nussinov, and Haim J. Wolfson
6. Indexing Protein Structures using Suffix Trees,
Feng Gao and Mohammed J. Zaki
Protein Features Prediction
7. Hidden Markov Models for Prediction of Protein Features,
Christopher Bystroff and Anders Krogh
8. The pros and cons of predicting protein contact maps,
Lisa Bartoli, Emidio Capriotti, Piero Fariselli,
Pier Luigi Martelli, and Rita Casadio
9. Roadmap Methods for Protein Folding,
Mark Moll, David Schwarz, Lydia E. Kavraki
Methods for de novo Structure Prediction
10. Scoring functions for de novo protein structure prediction
revisited, Shing-Chung Ngan, Ling-Hong Hung, Tianyun Liu, and
Ram Samudrala
11. Protein-Protein Docking: Overview and Performance Analysis,
Kevin Wiehe, Matthew W. Peterson, Brian Pierce, Julian Mintseris,
and Zhiping Weng
12. Molecular Dynamics Simulations of Protein Folding, Angel E. Garcia
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