Computational prediction of RNA-protein interaction partners and interfaces
نویسندگان
چکیده
v CHAPTER 1. GENERAL INTRODUCTION 1 Overall Goals 2 Dissertation Organization 3 References 5 CHAPTER 2. COMPUTATIONAL TOOLS FOR INVESTIGATING RNA-PROTEIN INTERACTION PARTNERS 7 Abstract 7 Introduction 8 RNA-Protein Partner Prediction Methods and Web Servers 9 Web servers for partner prediction 14 RNA-Protein Interface Prediction Methods 15 Sequence and structural motifs in RNA-protein interfaces 17 RNA-Protein Interaction Databases 18 PRD 20 NPInter 21 RPIntDB 21 PRIDB 22 RBPDB 22 Future Directions 23 Acknowledgements and Funding 24 Supplementary materials 25 Machine Learning Classifiers 25 Performance Evaluation Metrics 26 Comparison of RPISeq classifier with Wang et al.’s method 28 References 29 CHAPTER 3. PREDICTING RNA-PROTEIN INTERACTIONS USING ONLY SEQUENCE INFORMATION 34 Abstract 34 Background 34 Results 34 Conclusions 35 Background 35 Results 37 RPISeq classifiers can reliably predict RNA-protein interactions 39 Comparison with other methods for predicting RNA-protein interactions 41 Predicting ncRNA-protein interaction networks 43 Discussion 49 Sequence-based prediction of RNA-protein interactions 49
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