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Computational Prediction of Protein Complexes From Protein Interaction Networks【2025|PDF|Epub|mobi|kindle电子书版本百度云盘下载】

Computational Prediction of Protein Complexes From Protein Interaction Networks
  • Sriganesh Srihari 著
  • 出版社： Morgan & Claypool
  • ISBN：
  • 出版时间：2017
  • 标注页数：282页
  • 文件大小：125MB
  • 文件页数：299页
  • 主题词：

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图书目录

Chapter 1 Introduction to Protein Complex Prediction1

1.1 From Protein Interactions to Protein Complexes6

1.2 Databases for Protein Complexes11

1.3 Organization of the Rest of the Book13

Chapter 2 Constructing Reliable Protein-Protein Interaction （PPI） Networks15

2.1 High-Throughput Experimental Systems to Infer PPIs15

2.2 Data Sources for PPIs23

2.3 Topological Properties of PPI Networks25

2.4 Theoretical Models for PPI Networks27

2.5 Visualizing PPI Networks31

2.6 Building High-Confidence PPI Networks34

2.7 Enhancing PPI Networks by Integrating Functional Interactions50

Chapter 3 Computational Methods for Protein Complex Prediction from PPI Networks59

3.1 Basic Definitions and Terminologies60

3.2 Taxonomy of Methods for Protein Complex Prediction60

3.3 Methods Based Solely on PPI Network Clustering61

3.4 Methods Incorporating Core-Attachment Structure78

3.5 Methods Incorporating Functional Information85

Chapter 4 Evaluating Protein Complex Prediction Methods91

4.1 Evaluation Criteria and Methodology91

4.2 Evaluation on Unweighted Yeast PPI Networks93

4.3 Evaluation on Weighted Yeast PPI Networks95

4.4 Evaluation on Human PPI Networks99

4.5 Case Study：Prediction of the Human Mechanistic Target of Rapamycin Complex103

4.6 Take-Home Lessons from Evaluating Prediction Methods105

Chapter 5 Open Challenges in Protein Complex Prediction107

5.1 Three Main Challenges in Protein Complex Prediction107

5.2 Identifying Sparse Protein Complexes112

5.3 Identifying Overlapping Protein Complexes118

5.4 Identifying Small Protein Complexes124

5.5 Identifying Protein Sub-complexes134

5.6 An Integrated System for Identifying Challenging Protein Complexes136

5.7 Recent Methods for Protein Complex Prediction138

5.8 Identifying Membrane-Protein Complexes141

Chapter 6 Identifying Dynamic Protein Complexes145

6.1 Dynamism of Protein Interactions and Protein Complexes145

6.2 Identifying Temporal Protein Complexes149

6.3 Intrinsic Disorder in Proteins156

6.4 Intrinsic Disorder in Protein Interactions and Protein Complexes157

6.5 Identifying Fuzzy Protein Complexes162

Chapter 7 Identifying Evolutionarily Conserved Protein Complexes165

7.1 Inferring Evolutionarily Conserved PPIs （Interologs）166

7.2 Identifying Conserved Complexes from Interolog Networks，Ⅰ170

7.3 Identifying Conserved Complexes from Interolog Networks，Ⅱ178

Chapter 8 Protein Complex Prediction in the Era of Systems Biology185

8.1 Constructing the Network of Protein Complexes185

8.2 Identifying Protein Complexes Across Phenotypes189

8.3 Identifying Protein Complexes in Diseases192

8.4 Enhancing Quantitative Proteomics Using PPI Networks and Protein Complexes208

8.5 Systems Biology Tools and Databases to Analyze Biomolecular Networks221

Chapter 9 Conclusion225

References233

Authors’ Biographies279

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