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...

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Detalles Bibliográficos
Autor Corporativo: IEEE Engineering in Medicine and Biology Society (-)
Otros Autores: DasGupta, Bhaskar (Professor of computer science), autor (autor), Liang, Jie, 1964- autor
Formato: Libro electrónico
Idioma:Inglés
Publicado: Hoboken : Wiley : IEEE Press [2016]
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.