1;Cover;1 2;Title Page;5 3;Copyright;6 4;Contents;7 5;Preface of the First Edition;17 6;Preface of the Second Edition;19 7;Chapter 1 Networks in Biological Cells;21 7.1;1.1 Some Basics About Networks;21 7.1.1;1.1.1 Random Networks;22 7.1.2;1.1.2 Small?World Phenomenon;22 7.1.3;1.1.3 Scale?Free Networks;23 7.2;1.2 Biological Background;24 7.2.1;1.2.1 Transcriptional Regulation;25 7.2.2;1.2.2 Cellular Components;25 7.2.3;1.2.3 Spatial Organization of Eukaryotic Cells into Compartments;27 7.2.4;1.2.4 Considered Organisms;28 7.3;1.3 Cellular Pathways;28 7.3.1;1.3.1 Biochemical Pathways;28 7.3.2;1.3.2 Enzymatic Reactions;31 7.3.3;1.3.3 Signal Transduction;31 7.3.4;1.3.4 Cell Cycle;32 7.4;1.4 Ontologies and Databases;32 7.4.1;1.4.1 Ontologies;32 7.4.2;1.4.2 Gene Ontology;33 7.4.3;1.4.3 Kyoto Encyclopedia of Genes and Genomes;33 7.4.4;1.4.4 Reactome;33 7.4.5;1.4.5 Brenda;34 7.4.6;1.4.6 DAVID;34 7.4.7;1.4.7 Protein Data Bank;35 7.4.8;1.4.8 Systems Biology Markup Language;35 7.5;1.5 Methods for Cellular Modeling;37 7.6;1.6 Summary;37 7.7;1.7 Problems;37 7.8;Bibliography;38 8;Chapter 2 Structures of Protein Complexes and Subcellular Structures;41 8.1;2.1 Examples of Protein Complexes;42 8.1.1;2.1.1 Principles of Protein-Protein Interactions;44 8.1.2;2.1.2 Categories of Protein Complexes;47 8.2;2.2 Complexome: The Ensemble of Protein Complexes;48 8.2.1;2.2.1 Complexome of Saccharomyces cerevisiae;48 8.2.2;2.2.2 Bacterial Protein Complexomes;50 8.2.3;2.2.3 Complexome of Human;51 8.3;2.3 Experimental Determination of Three?Dimensional Structures of Protein Complexes;51 8.3.1;2.3.1 X?ray Crystallography;52 8.3.2;2.3.2 NMR;54 8.3.3;2.3.3 Electron Crystallography/Electron Microscopy;54 8.3.4;2.3.4 Cryo?EM;54 8.3.5;2.3.5 Immunoelectron Microscopy;55 8.3.6;2.3.6 Fluorescence Resonance Energy Transfer;55 8.3.7;2.3.7 Mass Spectroscopy;56 8.4;2.4 Density Fitting;58 8.4.1;2.4.1 Correlation?Based Density Fitting;58 8.5;2.5 Fourier Transformation;60 8.5.1;2.5.1 Fourier Series;60 8.5.2;2.5.2 Continuous Fourier Transform;61 8.5.3;2.5.3 Discrete Fourier Transform;61 8.5.4;2.5.4 Convolution Theorem;61 8.5.5;2.5.5 Fast Fourier Transformation;62 8.6;2.6 Advanced Density Fitting;64 8.6.1;2.6.1 Laplacian Filter;65 8.7;2.7 FFT Protein-Protein Docking;66 8.8;2.8 Protein-Protein Docking Using Geometric Hashing;68 8.9;2.9 Prediction of Assemblies from Pairwise Docking;69 8.9.1;2.9.1 CombDock;69 8.9.2;2.9.2 Multi?LZerD;72 8.9.3;2.9.3 3D?MOSAIC;72 8.10;2.10 Electron Tomography;73 8.10.1;2.10.1 Reconstruction of Phantom Cell;75 8.10.2;2.10.2 Protein Complexes in Mycoplasma pneumoniae;75 8.11;2.11 Summary;76 8.12;2.12 Problems;77 8.12.1;2.12.1 Mapping of Crystal Structures into EM Maps;77 8.13;Bibliography;80 9;Chapter 3 Analysis of Protein-Protein Binding;83 9.1;3.1 Modeling by Homology;83 9.2;3.2 Properties of Protein-Protein Interfaces;86 9.2.1;3.2.1 Size and Shape;86 9.2.2;3.2.2 Composition of Binding Interfaces;88 9.2.3;3.2.3 Hot Spots;89 9.2.4;3.2.4 Physicochemical Properties of Protein Interfaces;91 9.2.5;3.2.5 Predicting Binding Affinities of Protein-Protein Complexes;92 9.2.6;3.2.6 Forces Important for Biomolecular Association;93 9.3;3.3 Predicting Protein-Protein Interactions;95 9.3.1;3.3.1 Pairing Propensities;95 9.3.2;3.3.2 Statistical Potentials for Amino Acid Pairs;98 9.3.3;3.3.3 Conservation at Protein Interfaces;99 9.3.4;3.3.4 Correlated Mutations at Protein Interfaces;103 9.4;3.4 Summary;106 9.5;3.5 Problems;106 9.6;Bibliography;106 10;Chapter 4 Algorithms on Mathematical Graphs;109 10.1;4.1 Primer on Mathematical Graphs;109 10.2;4.2 A Few Words About Algorithms and Computer Programs;110 10.2.1;4.2.1 Implementation of Algorithms;111 10.2.2;4.2.2 Classes of Algorithms;112 10.3;4.3 Data Structures for Graphs;113 10.4;4.4 Dijkstra's Algorithm;115 10.4.1;4.4.1 Description of the Algorithm;116 10.4.2;4.4.2 Pseudocode;120 10.4.3;4.4.3 Running Time;121 10.5;4.5 Minimum Spanning Tree;121 10.5.1;4.5.1 Kruskal's Algorithm;122 10.6;4.6 Graph Drawing;122 10.7;4