臺灣博碩士論文加值系統

Electron transport chain, also known as the respiratory chain to provide energy for a chemical reaction organism, plays an integral role in the electron transport process to carry and transfer proteins. These proteins are called the electron transport proteins. The components of the electron transport chain are organized into 4 complexes: complex I, complex II, complex III and complex IV. The structure of protein depends on the interaction with other molecules (proteins, DNA, ligands and so on). Flavin adenine dinucleotide (FAD) is one of the important molecules; it is mainly in complex II of the electron transport protein. Understanding about FAD structure is necessary and important. Thus, predicting FAD binding is a very important task.
In this experiment, we use evolutionary information with QuickRBF classifier to predict the electron transport proteins and protein sequences of the FAD binding position, through analysis and statistics found in the electron transport protein of the FAD binding specificity to develop a specific model to predict FAD binding protein.

Electron transport chain, also known as the respiratory chain to provide energy for a chemical reaction organism, plays an integral role in the electron transport process to carry and transfer proteins. These proteins are called the electron transport proteins. The components of the electron transport chain are organized into 4 complexes: complex I, complex II, complex III and complex IV. The structure of protein depends on the interaction with other molecules (proteins, DNA, ligands and so on). Flavin adenine dinucleotide (FAD) is one of the important molecules; it is mainly in complex II of the electron transport protein. Understanding about FAD structure is necessary and important. Thus, predicting FAD binding is a very important task.
In this experiment, we use evolutionary information with QuickRBF classifier to predict the electron transport proteins and protein sequences of the FAD binding position, through analysis and statistics found in the electron transport protein of the FAD binding specificity to develop a specific model to predict FAD binding protein.

Tables of Figures vi
List of tables viii
Chapter 1 INTRODUCTION 1
1.1. Membrane protein 1
1.2. Electron transport chain 2
1.3. 4 complexes in electron transport chain 3
1.3.1. Complex I 4
1.3.2. Complex II 5
1.3.3. Complex III 6
1.3.4. Complex IV 6
1.4. FAD binding 7
1.5. The Organization of this Study 8
Chapter 2 LITERATURE REVIEW 9
2.1. Introduction 9
2.2. Related research on electron transport protein 9
2.3. Related research on FAD binding protein 10
2.4. The purpose of the study and motivation research 11
Chapter 3 METHODOLOGY 12
3.1. Data collection 12
3.1.1. Universal Protein Resource 12
3.1.2. Get data from UniProt 13
3.1.3. Get FAD binding from electron transport protein 15
3.1.4. Get FAD binding from another databases 17
3.1.5. Statistic all FAD binding proteins 19
3.2. Effectiveness Evaluation Method 22
3.3. Authentication method 23
3.4. PAM250 24
3.5. BLOSUM62 25
3.6. Position Specific Scoring Matrix (PSSM) 26
3.7. Classifiers 27
3.7.1. QuickRBF: 27
3.7.2. LibSVM 29
3.7.3. FADPred: A webserver for the prediction of FAD interacting 29
Chapter 4 RESULTS 31
1. Composition analysis 31
2. General FAD binding classifier 33
3. Use general FAD classifier to predict FAD in independent data 35
4. Predicting 7 FAD binding in electron transport protein (1 by 1) 35
Chapter V CONCLUSION 40
1. Research Contributions 40
2. Limitations and Further Study 40
References 42

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