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Principles of computational cell biology : from protein complexes to cellular networks / Volkhard Helms. — Weinheim : Wiley-VCH Verlag GmbH & Co. kGaA, c2008. – (58.157/H481) |
Contents
Contents
Preface XI
1 Networks in Biological Cells 1
1.1 Some Basics about Networks 1
1.2 Biological Background 4
1.3 Cellular Pathways 7
1.4 Ontologies and Databases 12
1.5 Methods in Cellular Modeling 14
2 Algorithms on Mathematical Graphs 17
2.1 Primer on Mathematical Graphs 17
2.2 A Few Words about Algorithms and Computer Programs 18
2.3 Data Structures for Graphs 21
2.4 Dijkstra's Algorithm 23
2.5 Minimum Spanning Tree 29
2.6 Graph Drawing 31
3 Protein-Protein Interaction Networks- Pairwise Connectivity 39
3.1 Principles of Protein-Protein Interactions 39
3.2 Experimental High-Throughput Methods for Detecting Protein-Protein Interactions 40
3.3 Bioinformatic Prediction of Protein-Protein Interactions 49
3.4 Bayesian Networks for Judging the Accuracy of Interactions 52
3.5 Protein Domain Networks 59
4 Protein-Protein Interaction Networks-Structural Hierarchies 67
4.1 Protein Interaction Graph Networks 67
4.2 Finding Cliques 71
4.3 Random Graphs 72
4.4 Scale-Free Graphs 73
4.5 Detecting Communities in Networks 75
4.6 Modular Decomposition 82
4.7 Network Growth Mechanisms 86
5 Gene Regulatory Networks 99
5.1 Regulation of Gene Transcription at Promoters 100
5.2 Gene Regulatory Networks 101
5.3 Graph Theoretical Models 105
5.4 Dynamic Models 106
5.5 Motifs 111
6 Metabolic Networks 115
6.1 Introduction 115
6.2 Stoichiometric Matrix 118
6.3 Linear Algebra Primer 121
6.4 Flux Balance Analysis 125
6.5 Double Description Method 128
6.6 Extreme Pathways and Elementary Modes 133
6.7 Minimal Cut Sets 140
6.8 High-Flux Backbone 146
7 Kinetic Modeling of Cellular Processes 155
7.1 Ordinary Differential Equation Models 155
7.2 Modeling Cellular Feedback Loops by ODEs 158
7.3 Partial Differential Equations 169
7.4 Dynamic Monte Carlo (Gillespie Algorithm) 172
7.5 Stochastic Modeling of a Small Molecular Network 173
7.6 Parameter Optimization with Genetic Algorithms 182
8 Structures of Protein Complexes and Subcellular Structures 193
8.1 Examples of Protein Complexes 193
8.2 Complexeome of S. cerevisiae 197
8.3 Experimental Determination of Three-dimensional Structures of Protein Complexes 199
8.4 Density Fitting 204
8.5 Fourier Transformation 206
8.6 Advanced Density Fitting 210
8.7 FFT Protein-Protein Docking 216
8.8 Prediction of Assemblies from Pairwise Docking 218
8.9 Electron Tomography 221
9 Biomolecular Association and Binding 231
9.1 Modeling by Homology 231
9.2 Structural Properties of Protein-Protein Interfaces 233
9.3 Bioinformatic Prediction of Protein-Protein Interfaces 239
9.4 Forces Important for Biomolecular Association 246
9.5 Protein-Protein Association 249
9.6 Assembly of Macromolecular Complexes: the Ribosome 254
10 Integrated Networks 261
10.1 Correlating Interactome and Gene Regulation 261
10.2 Response of Gene Regulatory Network to Outside Stimuli 263
10.3 Integrated Analysis of Metabolic and Regulatory Networks 266
11 Outlook 271
Index 273
