Models and algorithms for biomolecules and molecular networks
By providing expositions to modeling principles, theories, computational solutions, and open problems, this reference presents a full scope on relevant biological phenomena, modeling frameworks, technical challenges, and algorithms.-Up-to-date developments of structures of biomolecules, systems biol...
Autor Corporativo: | |
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Otros Autores: | , |
Formato: | Libro electrónico |
Idioma: | Inglés |
Publicado: |
Hoboken :
Wiley : IEEE Press
[2016]
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Colección: | Wiley ebooks.
IEEE Press Series in Biomedical Engineering. |
Acceso en línea: | Conectar con la versión electrónica |
Ver en Universidad de Navarra: | https://innopac.unav.es/record=b40610214*spi |
Tabla de Contenidos:
- List of Figures xiii
- List of Tables xix
- Foreword xxi
- Acknowledgments xxiii
- 1 Geometric Models of Protein Structure and Function Prediction 1
- 1.1 Introduction, 1
- 1.2 Theory and Model, 2
- 1.2.1 Idealized Ball Model, 2
- 1.2.2 Surface Models of Proteins, 3
- 1.2.3 Geometric Constructs, 4
- 1.2.4 Topological Structures, 6
- 1.2.5 Metric Measurements, 9
- 1.3 Algorithm and Computation, 13
- 1.4 Applications, 15
- 1.4.1 Protein Packing, 15
- 1.4.2 Predicting Protein Functions from Structures, 17
- 1.5 Discussion and Summary, 20
- References, 22
- Exercises, 25
- 2 Scoring Functions for Predicting Structure and Binding of Proteins 29
- 2.1 Introduction, 29
- 2.2 General Framework of Scoring Function and Potential Function, 31
- 2.2.1 Protein Representation and Descriptors, 31
- 2.2.2 Functional Form, 32
- 2.2.3 Deriving Parameters of Potential Functions, 32
- 2.3 Statistical Method, 32
- 2.3.1 Background, 32
- 2.3.2 Theoretical Model, 33
- 2.3.3 Miyazawa
- Jernigan Contact Potential, 34
- 2.3.4 Distance-Dependent Potential Function, 41
- 2.3.5 Geometric Potential Functions, 45
- 2.4 Optimization Method, 49
- 2.4.1 Geometric Nature of Discrimination, 50
- 2.4.2 Optimal Linear Potential Function, 52
- 2.4.3 Optimal Nonlinear Potential Function, 53
- 2.4.4 Deriving Optimal Nonlinear Scoring Function, 55
- 2.4.5 Optimization Techniques, 55
- 2.5 Applications, 55
- 2.5.1 Protein Structure Prediction, 56
- 2.5.2 Protein
- Protein Docking Prediction, 56
- 2.5.3 Protein Design, 58
- 2.5.4 Protein Stability and Binding Affinity, 59
- 2.6 Discussion and Summary, 60
- 2.6.1 Knowledge-Based Statistical Potential Functions, 60
- 2.6.2 Relationship of Knowledge-Based Energy Functions and Further Development, 64
- 2.6.3 Optimized Potential Function, 65
- 2.6.4 Data Dependency of Knowledge-Based Potentials, 66
- References, 67
- Exercises, 75
- 3 Sampling Techniques: Estimating Evolutionary Rates and Generating Molecular Structures 79.
- 3.1 Introduction, 79
- 3.2 Principles of Monte Carlo Sampling, 81
- 3.2.1 Estimation Through Sampling from Target Distribution, 81
- 3.2.2 Rejection Sampling, 82
- 3.3 Markov Chains and Metropolis Monte Carlo Sampling, 83
- 3.3.1 Properties of Markov Chains, 83
- 3.3.2 Markov Chain Monte Carlo Sampling, 85
- 3.4 Sequential Monte Carlo Sampling, 87
- 3.4.1 Importance Sampling, 87
- 3.4.2 Sequential Importance Sampling, 87
- 3.4.3 Resampling, 91
- 3.5 Applications, 92
- 3.5.1 Markov Chain Monte Carlo for Evolutionary Rate Estimation, 92
- 3.5.2 Sequentail Chain Growth Monte Carlo for Estimating Conformational Entropy of RNA Loops, 95
- 3.6 Discussion and Summary, 96
- References, 97
- Exercises, 99
- 4 Stochastic Molecular Networks 103
- 4.1 Introduction, 103
- 4.2 Reaction System and Discrete Chemical Master Equation, 104
- 4.3 Direct Solution of Chemical Master Equation, 106
- 4.3.1 State Enumeration with Finite Buffer, 106
- 4.3.2 Generalization and Multi-Buffer dCME Method, 108
- 4.3.3 Calculation of Steady-State Probability Landscape, 108
- 4.3.4 Calculation of Dynamically Evolving Probability Landscape, 108
- 4.3.5 Methods for State Space Truncation for Simplification, 109
- 4.4 Quantifying and Controlling Errors from State Space Truncation, 111
- 4.5 Approximating Discrete Chemical Master Equation, 114
- 4.5.1 Continuous Chemical Master Equation, 114
- 4.5.2 Stochastic Differential Equation: Fokker
- Planck Approach, 114
- 4.5.3 Stochastic Differential Equation: Langevin Approach, 116
- 4.5.4 Other Approximations, 117
- 4.6 Stochastic Simulation, 118
- 4.6.1 Reaction Probability, 118
- 4.6.2 Reaction Trajectory, 118
- 4.6.3 Probability of Reaction Trajectory, 119
- 4.6.4 Stochastic Simulation Algorithm, 119
- 4.7 Applications, 121
- 4.7.1 Probability Landscape of a Stochastic Toggle Switch, 121
- 4.7.2 Epigenetic Decision Network of Cellular Fate in Phage Lambda, 123
- 4.8 Discussions and Summary, 127
- References, 128.