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Language(s):
eng - English
Dates:
2009-12-10
Publication Status:
Accepted / In Press
Pages:
143
Publishing info:
Berlin : Freie Universität Berlin
Table of Contents:
Abstract 5
Acknowledgements 9
1 Introduction 13
1.1 A greater picture of systems biology . . . 13
1.1.1 A declaration and a virtual human . . . . 13
1.1.2 Double helix { single sequence . . . . . 13
1.1.3 From sequence to regulation . . . . . . . 15
1.1.4 Regulation and interaction in the cellular apparatus 15
1.1.5 Personalized Medicine . . . . . . . . . . 17
1.2 Loose ends . . . . . . .. . . . . . . . . . 18
1.2.1 An integration gap: elements, processes and methods 18
1.2.2 Biomolecules, string encoding and applications . . 19
1.2.3 Cell signaling . . . . . . . . . . .... . . . . . . 21
1.3 Objectives and overview . . . . . . . . . . . . . . . 23
2 Integration of ligand characteristics ..................25
2.1 Data warehouse of metabolite and drug binding sites: SuperSite 25
2.1.1 Introduction . . . . . ........ . . . . . . . . . . 25
2.1.2 Database and tools . . . . . . . . . . . .. . . . . 27
2.1.3 Case studies . . . . . . . . . . .. . . . . . . . . 29
2.1.4 Conclusions . . . . . . . . . . . . . ..... . . . . 31
2.2 A metaserver for structural search: Superimpos e . . 33
2.2.1 Introduction . . . . . . . . . . . . . . . . . . .. 33
2.2.2 Algorithms . . . . . . . . . . . . . . . . . . . .. 35
2.2.3 Databases . . . . . . . . . . . . . . . . . . . . . 39
2.2.4 Web server description . . . . . . . . . . . . . . 41
2.2.5 Case studies . . . . . . . . . . . . . . . . . . . 42
2.2.6 Conclusions . . . . . . . . . . . . . . . . . . . . 43
12 Contents
3 Biomolecular search, similarity and coding properties ..47
3.1 RNA character encoding and su x techniques . . .. . . 47
3.1.1 Introduction . . . . . . . . . . . . . . . . . . . 47
3.1.2 Methods . . . . . . . . . . . . . . . . . . . . . . 50
3.1.3 Results . . . . . . . . . . . . . . . . . . . . . . 54
3.1.4 Discussion . . . . . . . . . . . . . . . . . . . . 62
3.1.5 Conclusions . . . . . . . . . . . . . . . . . . . . 63
3.2 Macromolecular similarity screening . . . . . . . . . 64
3.2.1 Introduction . . . . . . . . . . .. . . . . . . . . 64
3.2.2 Material and methods . . . . . . . . .... . . . . . 68
3.2.3 Results . . . . . . . . . . . . . . . . . . . . . . 73
3.2.4 Discussion . . . . . . . . . . . . . .. . . . . . . 78
3.2.5 Conclusions . . . . . . . . . . . . . . . . . . . . 81
3.3 A novel approach for the detection of structural features of RNA ..........................................83
3.3.1 Introduction . . . . . . . . . . ...... . . . . . . 83
3.3.2 Material and methods . . . . . . . . . . . .. . . . 85
3.3.3 Results . . . . . . . . . . . . . . . . . . . . . . 86
3.3.4 Discussion . . . . . . . . . . . . . . . . . . . . 90
3.3.5 Conclusions . . . . . . . . . . . . . . . . . . . . 92
4 Simulation of cellular reactions .......................93
4.1 Quantitative simulation of apoptosis using Petri nets 93
4.1.1 Introduction . . . . . . . . . . . . . . . . . . . .93
4.1.2 Petri nets in systems biology . . . . . . . . . . . 94
4.1.3 Material and methods . . . . . . . . . . . .. . . . 96
4.1.4 Results . . . . . . . . . . . . . . . . . . . . . . 99
4.1.5 Discussion and future directions . . . . . . . . . 101
4.1.6 Conclusions . . . . . . . . . . . . . . . . . . . 104
4.2 Cell Sim {a Petri net based cell simulation software 105
4.2.1 Introduction . . . . . . . . . . . . . . . . . . . 105
4.2.2 Material and methods . . . . . . . . . . . . . . . 105
4.2.3 Results . . . . . . . . . . . . . . . . . . . . . 106
4.2.4 Discussion and conclusions . . . . . . . . . . . . 106
5 Discussion 111
6 Appendix 115
Ehrenwortliche Erklarung . . . . . . . . . . . . . . . 115
Zusammenfassung . . . . . . . . . . . . . . . . . . . . 116
Curriculum Vitae . . . . . . . . . . . . . . . . . . . . 117
List of gures . . . . . . . . . . . . . . . . . . . . . 118
List of tables . . . . . . . . . . . . . . . . . . . . . 122
Bibliography . . . . . . . . . . . . . . . . . . . . . . 123
Rev. Type:
-
Identifiers:
eDoc: 446314
Degree:
PhD
