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Computational Methods for Protein Structure Prediction and Modeling

von
Xu, YingHrsg.Xu, DongHrsg.Liang, JieHrsg.
E-BookPDF1 - PDF WatermarkE-Book
396 Seiten
Englisch
Springer New Yorkerschienen am24.08.20072007
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.


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.mehr
Verfügbare Formate
BuchKartoniert, Paperback
EUR160,49
BuchGebunden
EUR172,50
E-BookPDF1 - PDF WatermarkE-Book
EUR149,79
E-BookPDF1 - PDF WatermarkE-Book
EUR149,79

Produkt

KlappentextVolume 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.


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.
Details
Weitere ISBN/GTIN9780387683720
ProduktartE-Book
EinbandartE-Book
FormatPDF
Format Hinweis1 - PDF Watermark
FormatE107
Erscheinungsjahr2007
Erscheinungsdatum24.08.2007
Auflage2007
ReiheBiological and Medical Physics, Biomedical Engineering
Seiten396 Seiten
SpracheEnglisch
IllustrationenXX, 396 p. 88 illus.
Artikel-Nr.1424482
Rubriken
Genre9200

Inhalt/Kritik

Inhaltsverzeichnis
1;Preface;6
2;Acknowledgments;13
3;Contents;14
4;Contributors;16
5;1 A Historical Perspective and Overview of Protein Structure Prediction;20
5.1;1.1 Introduction;20
5.2;1.2 The Development of Protein Structure Prediction Methodologies;22
5.3;1.3 A Shift in the Focus for Protein Modeling;35
5.4;1.4 Summary;50
5.5;References;51
6;2 Empirical Force Fields;63
6.1;2.1 Potential Energy Functions;63
6.2;2.2 Implementation of Potential Energy Functions;66
6.3;2.3 Treatment of Aqueous Solvation;67
6.4;2.4 Empirical Force Field Optimization;69
6.5;2.5 Protein Force Fields;72
6.6;2.6 Extended or United Atom Protein Force Fields;76
6.7;2.7 Summary;77
6.8;Acknowledgments;77
6.9;Appendix;78
6.10;References;78
7;3 Knowledge-Based Energy Functions for Computational Studies of Proteins;88
7.1;3.1 Introduction;88
7.2;3.2 General Framework;89
7.3;3.3 Statistical Method;91
7.4;3.4 Optimization Method;110
7.5;3.5 Applications;118
7.6;3.6 Online Resources;124
7.7;3.7 Discussion;124
7.8;3.8 Summary;132
7.9;3.9 Further Reading;132
7.10;Acknowledgments;133
7.11;References;133
8;4 Computational Methods for Domain Partitioning of Protein Structures;141
8.1;4.1 Introduction;141
8.2;4.2 Definitions of Structural Domains;142
8.3;4.3 Computational Methods;144
8.4;4.4 In-depth Look into Algorithmic Domain Decomposition;151
8.5;4.5 Evaluating Automatic Methods with Manual Consensus Benchmark;155
8.6;4.6 Future Goals;158
8.7;4.7 Summary;159
8.8;4.8 Suggested Further Reading;159
8.9;References;160
9;5 Protein Structure Comparison and Classification;162
9.1;5.1 Introduction;162
9.2;5.2 Pairwise Alignment of Protein Structures;164
9.3;5.3 Multiple Structure Comparison and Structural Motif Search;172
9.4;5.4 Structure Search in Protein Databases;175
9.5;5.5 Protein Classification;180
9.6;5.6 Concluding Remarks;188
9.7;5.7 References and Resources;189
9.8;5.8 Further Reading;190
9.9;Acknowledgment;191
9.10;References;191
10;6 Computation of Protein Geometry and Its Applications: Packing and Function Prediction;196
10.1;6.1 Introduction;196
10.2;6.2 Theory and Model;197
10.3;6.3 Computation and Software;206
10.4;6.4 Applications: Packing Analysis;209
10.5;6.5 Applications: Protein Function Prediction from Structures;211
10.6;6.6 Discussion;215
10.7;6.7 Summary;216
10.8;6.8 Further Reading;217
10.9;Acknowledgments;217
10.10;References;217
11;7 Local Structure Prediction of Proteins;222
11.1;7.1 Introduction;222
11.2;7.2 Protein Secondary Structure Prediction;222
11.3;7.3 Protein Supersecondary Structure Prediction;236
11.4;7.4 Protein Disordered Region Detection;239
11.5;7.5 Internal Repeats Detection;241
11.6;7.6 Applications to Multiple Sequence Alignment;243
11.7;7.7 Applications to Local Protein Tertiary Structure Prediction;245
11.8;7.8 Software Packages;247
11.9;7.9 Resources;258
11.10;7.10 Summary;258
11.11;References;258
11.12;Further Reading;269
12;8 Protein Contact Map Prediction;270
12.1;8.1 Introduction;270
12.2;8.2 Definition of Interresidue Contacts and Contact Maps;270
12.3;8.3 Features of a Contact Map;272
12.4;8.4 From Contact Map Prediction to 3D Structure;275
12.5;8.5 Contact Map Prediction;277
12.6;8.6 Evaluation of Contact Map Predictions;285
12.7;8.7 Other Applications of Contact Maps;286
12.8;8.8 Conclusions;287
12.9;Recommended Reading;288
12.10;References;288
13;9 Modeling Protein Aggregate Assembly and Structure;293
13.1;9.1 Introduction;293
13.2;9.2 Folding and Misfolding;294
13.3;9.3 Experimental Approaches to Aggregate Structure;298
13.4;9.4 Computational Approaches to Aggregate Structure;305
13.5;9.5 Summary;318
13.6;Suggested Further Reading;319
13.7;Acknowledgments;319
13.8;References;319
14;10 Homology-Based Modeling of Protein Structure;332
14.1;10.1 Introduction;332
14.2;10.2 Procedures in Homology Modeling;336
14.3;10.3 Homology Modeling with JACKAL;351
14.4;10.4 Application of Homology Modeling;358
14.5;10.5 Summary;360
14.6;Further Reading;361
14.7;Acknowledgments;361
14.8;References;362
15;11 Modeling Protein Structures Based on Density Maps at Intermediate Resolutions;371
15.1;11.1 Introduction;371
15.2;11.2 Sheetminer: Locating Sheets in Intermediate- Resolution Density Maps;372
15.3;11.3 Sheettracer: Building Pseudo-traces for ß-Strands in Intermediate-Resolution Density Maps;378
15.4;11.4 Determining Protein Topology Based on Skeletons of Secondary Structures;385
15.5;11.5 Future Perspectives;396
15.6;Acknowledgment;397
15.7;References;397
16;Index;401mehr

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