Читать книгу Computational Prediction of Protein Complexes from Protein Interaction Networks - Sriganesh Srihari - Страница 7
Оглавление| Contents | |
| Preface | |
| Chapter 1 | Introduction to Protein Complex Prediction |
| 1.1 From Protein Interactions to Protein Complexes | |
| 1.2 Databases for Protein Complexes | |
| 1.3 Organization of the Rest of the Book | |
| Chapter 2 | Constructing Reliable Protein-Protein Interaction (PPI) Networks |
| 2.1 High-Throughput Experimental Systems to Infer PPIs | |
| 2.2 Data Sources for PPIs | |
| 2.3 Topological Properties of PPI Networks | |
| 2.4 Theoretical Models for PPI Networks | |
| 2.5 Visualizing PPI Networks | |
| 2.6 Building High-Confidence PPI Networks | |
| 2.7 Enhancing PPI Networks by Integrating Functional Interactions | |
| Chapter 3 | Computational Methods for Protein Complex Prediction from PPI Networks |
| 3.1 Basic Definitions and Terminologies | |
| 3.2 Taxonomy of Methods for Protein Complex Prediction | |
| 3.3 Methods Based Solely on PPI Network Clustering | |
| 3.4 Methods Incorporating Core-Attachment Structure | |
| 3.5 Methods Incorporating Functional Information | |
| Chapter 4 | Evaluating Protein Complex Prediction Methods |
| 4.1 Evaluation Criteria and Methodology | |
| 4.2 Evaluation on Unweighted Yeast PPI Networks | |
| 4.3 Evaluation on Weighted Yeast PPI Networks | |
| 4.4 Evaluation on Human PPI Networks | |
| 4.5 Case Study: Prediction of the Human Mechanistic Target of Rapamycin Complex | |
| 4.6 Take-Home Lessons from Evaluating Prediction Methods | |
| Chapter 5 | Open Challenges in Protein Complex Prediction |
| 5.1 Three Main Challenges in Protein Complex Prediction | |
| 5.2 Identifying Sparse Protein Complexes | |
| 5.3 Identifying Overlapping Protein Complexes | |
| 5.4 Identifying Small Protein Complexes | |
| 5.5 Identifying Protein Sub-complexes | |
| 5.6 An Integrated System for Identifying Challenging Protein Complexes | |
| 5.7 Recent Methods for Protein Complex Prediction | |
| 5.8 Identifying Membrane-Protein Complexes | |
| Chapter 6 | Identifying Dynamic Protein Complexes |
| 6.1 Dynamism of Protein Interactions and Protein Complexes | |
| 6.2 Identifying Temporal Protein Complexes | |
| 6.3 Intrinsic Disorder in Proteins | |
| 6.4 Intrinsic Disorder in Protein Interactions and Protein Complexes | |
| 6.5 Identifying Fuzzy Protein Complexes | |
| Chapter 7 | Identifying Evolutionarily Conserved Protein Complexes |
| 7.1 Inferring Evolutionarily Conserved PPIs (Interologs) | |
| 7.2 Identifying Conserved Complexes from Interolog Networks, I | |
| 7.3 Identifying Conserved Complexes from Interolog Networks, II | |
| Chapter 8 | Protein Complex Prediction in the Era of Systems Biology |
| 8.1 Constructing the Network of Protein Complexes | |
| 8.2 Identifying Protein Complexes Across Phenotypes | |
| 8.3 Identifying Protein Complexes in Diseases | |
| 8.4 Enhancing Quantitative Proteomics Using PPI Networks and Protein Complexes | |
| 8.5 Systems Biology Tools and Databases to Analyze Biomolecular Networks | |
| Chapter 9 | Conclusion |
| References | |
| Authors’ Biographies |
