| Abstract | 第4-5页 |
| 摘要 | 第6-11页 |
| Contents | 第11-14页 |
| Chapter 1 Introduction | 第14-42页 |
| 1.1 Computational Biology Data Source | 第16-22页 |
| 1.1.1 Nucleotide Sequence Databases | 第18页 |
| 1.1.2 Protein Sequence Databases | 第18-20页 |
| 1.1.3 Protein Domain & Family Databases | 第20页 |
| 1.1.4 Structure- Based Databases | 第20-22页 |
| 1.2 Protein Sequence Clustering | 第22-29页 |
| 1.2.1 The Problems of Protein Sequence Clustering | 第23-26页 |
| 1.2.2 Existing Methods of Protein Sequence Clustering | 第26-29页 |
| 1.3 Comparative Modeling | 第29-37页 |
| 1.3.1 Protein Structure Prediction | 第29-32页 |
| 1.3.2 Stages in Comparative Modeling Process | 第32-37页 |
| 1.4 Prediction of Protein-Protein Interaction | 第37-42页 |
| 1.4.1 Evolutionary Traces in Protein-Protein Interaction | 第38-39页 |
| 1.4.2 Prediction of Interacting Regions | 第39-40页 |
| 1.4.3 Prediction of Interacting Proteins | 第40-42页 |
| Chapter 2 Clustering Orthologs Based on Sequence and Domain Similarities | 第42-64页 |
| 2.1 Introduction | 第43-47页 |
| 2.2 Previous Works | 第47-51页 |
| 2.2.1 The Database of Orthologous Clusters | 第47-49页 |
| 2.2.2 Related Methods for Clustering of Orthologous Groups | 第49-51页 |
| 2.3 Materials and Methods | 第51-57页 |
| 2.3.1 Sequence Data and Alignment Score Refinements | 第52-54页 |
| 2.3.2 Clustering | 第54-56页 |
| 2.3.3 Validation of Clusters | 第56-57页 |
| 2.4 Results | 第57-61页 |
| 2.5 Conclusion | 第61-64页 |
| Chapter 3 The Integration of Protein Interaction Information | 第64-77页 |
| 3.1 Background | 第64-66页 |
| 3.2 Materials and Methods | 第66-69页 |
| 3.2.1 Datasets | 第66-67页 |
| 3.2.2 Interaction Confidence Score | 第67-68页 |
| 3.2.3 Optimization by Evolutionary Strategy | 第68-69页 |
| 3.3 Results and Discussions | 第69-75页 |
| 3.3.1 Validation of Confidence Scores | 第69-73页 |
| 3.3.2 Yeast Gene-Gene Interaction Network Is Scale-Free | 第73-75页 |
| 3.3.3 Assessment of the Reliability of Method | 第75页 |
| 3.4 Conclusion | 第75-77页 |
| Chapte14 Comparative Modeling Based on Sequence-Conserved Domains | 第77-100页 |
| 4.1 Introduction | 第77-81页 |
| 4.2 Progresses and Remaining Problems in Comparative Modeling | 第81-86页 |
| 4.2.1 Sequence Similarity | 第81页 |
| 4.2.2 Template Recognition | 第81-83页 |
| 4.2.3 The alignment in Comparative Modeling | 第83-85页 |
| 4.2.4 The Modeling | 第85-86页 |
| 4.3 Experimental Design | 第86-91页 |
| 4.3.1 Template Library of Structural Clusters for Sequence-Conserved Domains | 第87-88页 |
| 4.3.2 Structure-Anchored Alignment | 第88-90页 |
| 4.3.3 Benchmark Selection and Validation | 第90-91页 |
| 4.4 Results and Discussions | 第91-98页 |
| 4.4.1 Structure Information of the Templates Library | 第91-95页 |
| 4.4.2 Comparison of Results Predicted Using Different Alignment Protocols | 第95-98页 |
| 4.5 Conclusion | 第98-100页 |
| Chapter 5 Structure-Based Assembly of Protein Interaction Network | 第100-112页 |
| 5.1 Background | 第101-102页 |
| 5.2 Methods and Materials | 第102-106页 |
| 5.2.1 Overview of the Methodology | 第102-103页 |
| 5.2.2 Datasets of Protein Interactions and Predicted Domain Structures | 第103-104页 |
| 5.2.3 Building a Domain-Domain Interaction Map | 第104-106页 |
| 5.2.4 Inferring Biological Consistence of the Homologous Complexes | 第106页 |
| 5.3 Results and Discussion | 第106-112页 |
| 5.3.1 the Characterized Domain-Domain Interaction | 第106-108页 |
| 5.3.2 Validation the Method Using a Structure-Known Complex as Benchmark | 第108-109页 |
| 5.3.3 Demonstration the Consistencies of Domain-Domain Docking | 第109-112页 |
| Chapter 6 Conclusion | 第112-115页 |
| 6.1 the Significance of This Study | 第112页 |
| 6.2 Overall Goal and Results | 第112-113页 |
| 6.3 Future Works | 第113-115页 |
| Appendix A Parallel Bio-Sequence Comparison based on Smith-Waterman Algorithm | 第115-127页 |
| A1 Introduction | 第115-117页 |
| A2 The Smith-Waterman Algorithm | 第117-120页 |
| A2.1 Pair-Wise sequence Alignment | 第117-118页 |
| A2.2 Smith-Waterman Algorithm | 第118-120页 |
| A3 Parallel Pair-Wire Alignment Algorithm Based on Smith-Waterman Algorithm | 第120-124页 |
| A3.1 The PSW-DC Algorithm | 第120-121页 |
| A3.2 The C&E Method | 第121-124页 |
| A4. Experimental Results | 第124-125页 |
| A5. Conclusion and Further Work | 第125-127页 |
| Reference | 第127-138页 |
| Resume | 第138-140页 |
| Acknowledgements | 第140页 |
