Cover image for Computational methods for protein structure prediction and modeling
Title:
Computational methods for protein structure prediction and modeling
Series:
Biological and medical physics, biomedical engineering
Publication Information:
New York, NY : Springer, 2007
Physical Description:
v.
ISBN:
9780387333199

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Material Type
Item Category 1
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30000010133234 QD431.25.S85 C65 2007 v.1 Open Access Book Book
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30000010151059 QD431.25.S85 C65 2007 v.2 Open Access Book Book
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Summary

Summary

Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.


Author Notes

Dr. Ying Xu is Regents-GRA Eminent Scholar and Professor at the University of Georgia. Dr. Dong Xu is the Director of the Digital Biology Laboratory at the University of Missouri-Columbia. Dr. Jie Liang is the Director for the Center for Bioinformatics at the University of Illinois at Chicago.


Table of Contents

John C. Wooley and Yuzhen YeAlexander D. MacKerell, Jr.Xiang Li and Jie LiangStella Veretnik and Ilya ShindyalovOrhan Camoglu and Ambuj K. SinghJie LiangVictor A. Simossis and Jaap HeringaXin Yuan and Christopher BystroffJun-tao Guo and Carol K. Hall and Ying Xu and Ronald B. WetzelZhexin XiangJianpeng Ma
Contributorsp. xvii
1 A Historical Perspective and Overview of Protein Structure Predictionp. 1
2 Empirical Force Fieldsp. 45
3 Knowledge-Based Energy Functions for Computational Studies of Proteinsp. 71
4 Computational Methods for Domain Partitioning of Protein Structuresp. 125
5 Protein Structure Comparison and Classificationp. 147
6 Computation of Protein Geometry and Its Applications: Packing and Function Predictionp. 181
7 Local Structure Prediction of Proteinsp. 207
8 Protein Contact Map Predictionp. 255
9 Modeling Protein Aggregate Assembly and Structurep. 279
10 Homology-Based Modeling of Protein Structurep. 319
11 Modeling Protein Structures Based on Density Maps at Intermediate Resolutionsp. 359
Indexp. 389