A Metaheuristic Approach to Protein Structure Prediction - Nanda Dulal Jana, Swagatam Das, Jaya Sil Blick ins Buch

A Metaheuristic Approach to Protein Structure Prediction (eBook)

Algorithms and Insights from Fitness Landscape Analysis

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eBook Download: PDF
2018 | 1st ed. 2018
XXIX, 220 Seiten
Springer International Publishing (Verlag)
978-3-319-74775-0 (ISBN)

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A Metaheuristic Approach to Protein Structure Prediction - Nanda Dulal Jana, Swagatam Das, Jaya Sil
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This book introduces characteristic features of the protein structure prediction (PSP) problem. It focuses on systematic selection and improvement of the most appropriate metaheuristic algorithm to solve the problem based on a fitness landscape analysis, rather than on the nature of the problem, which was the focus of methodologies in the past.

 Protein structure prediction is concerned with the question of how to determine the three-dimensional structure of a protein from its primary sequence. Recently a number of successful metaheuristic algorithms have been developed to determine the native structure, which plays an important role in medicine, drug design, and disease prediction.

 This interdisciplinary book consolidates the concepts most relevant to protein structure prediction (PSP) through global non-convex optimization. It is intended for graduate students from fields such as computer science, engineering, bioinformatics and as a reference for researchers and practitioners.




Foreword 6
Preface 8
Contents 13
Abbreviations and Symbols 17
List of Figures 19
List of Tables 24
List of Algorithms 27
1 Backgrounds on Protein Structure Prediction and Metaheuristics 28
1.1 Introduction 28
1.2 Proteins and Amino Acids 30
1.3 Level of Protein Structures 31
1.3.1 Primary Structure 31
1.3.2 Secondary Structure 32
1.3.3 Tertiary Structure 33
1.3.4 Quaternary Structure 33
1.4 Protein Structure Prediction 33
1.5 Protein Structure Prediction Methods 33
1.5.1 Experimental Methods 33
1.5.2 Computational Methods 34
1.6 Computational Model 35
1.6.1 HP Lattice Model 35
1.6.2 AB Off-Lattice Model 36
1.7 Population Based Metaheuristic Techniques 39
1.7.1 An Optimization Problem 40
1.7.2 The Metaheuristic Family 40
1.7.3 The Evolutionary Algorithms 41
1.7.4 Swarm Intelligence Algorithms 46
1.7.5 Physical Phenomena Based Algorithms 50
1.8 Innovation and Research: Main Contribution of This Volume 55
2 Metaheuristic Approach to PSP—An Overview of the Existing State-of-the-art 56
2.1 Introduction 56
2.2 Evolution Based Metaheuristic Algorithms 57
2.3 Swarm Intelligence Based Metaheuristic Algorithms 59
2.4 Physical Phenomena Based Metaheuristic Algorithms 61
2.5 Hybrid Algorithms 62
2.6 Protein Structure Prediction Using Metaheuristics: A Road Map of This Volume 63
2.7 Potential Applications Areas for the Metaheuristics Based Structure Prediction 64
3 Continuous Landscape Analysis Using Random Walk Algorithm 66
3.1 Introduction 66
3.2 Simple Random Walk (SRW) 68
3.3 Random Walks for Fitness Landscapes Analysis 70
3.4 Chaotic Map 70
3.4.1 Logistic Map 71
3.4.2 Tent Map 71
3.4.3 Chebyshev Map 71
3.4.4 Cubic Map 71
3.4.5 ICMIC Map 72
3.5 Landscape Measure Indices 73
3.5.1 Entropy Based Measure 73
3.5.2 Fitness Distance Correlation (FDC) 74
3.6 The Chaotic Random Walk (CRW) Algorithm 74
3.6.1 Chaotic Pseudo Random Number (CPRN) Generation 75
3.6.2 Chaos Based Random Walk Algorithm 75
3.6.3 Coverage Analysis of the Walks 78
3.7 Experiments for the Benchmark Functions 81
3.7.1 Benchmark Functions 81
3.7.2 Simulation Configurations 81
3.7.3 Results and Discussion 82
3.7.4 Landscape Analysis for 20-Dimension 90
3.8 Application to PSP Problem 108
3.9 Summary 111
4 Landscape Characterization and Algorithms Selection for the PSP Problem 113
4.1 Introduction 113
4.2 Fitness Landscape Measures 115
4.2.1 Information Based Measure 116
4.2.2 Statistical Measure 119
4.3 Energy Function Landscape Structure 120
4.3.1 Quasi-Random Sampling 121
4.3.2 Landscape Path Creation 122
4.4 Landscape Analysis for PSP Problem 123
4.4.1 Experimental Settings 123
4.4.2 Results and Discussion 125
4.5 Performance Analysis of the Metaheuristic Algorithms 150
4.5.1 Simulation Configurations 150
4.5.2 Performance Measures 152
4.5.3 Results and Discussion 153
4.6 Summary 176
5 The Lévy Distributed Parameter Adaptive Differential Evolution for Protein Structure Prediction 177
5.1 Introduction 177
5.2 Lévy Distributed DE (LdDE) 179
5.2.1 Lévy Distribution 179
5.2.2 The Lévy Distributed DE Algorithm 181
5.3 Experimental Results 182
5.3.1 Benchmark Functions 182
5.3.2 Simulation Strategy 183
5.3.3 Results and Discussion 184
5.4 Application to Protein Structure Prediction 189
5.4.1 Simulation Strategy 189
5.4.2 Results and Discussion 190
5.5 Summary 193
6 Protein Structure Prediction Using Improved Variants of Metaheuristic Algorithms 194
6.1 Introduction 194
6.2 Particle Swarm Optimization with Local Search 195
6.2.1 Hill Climbing: A Local Search Algorithm 196
6.2.2 PSOLS Algorithm 197
6.2.3 Experimental Results 198
6.3 The Mutation Based Bees Algorithm 202
6.3.1 Adaptive Polynomial Mutation Based BA 204
6.3.2 Experimental Results 205
6.4 The Chaos-Based Biogeography Based Optimization Algorithm 208
6.4.1 Chaotic Mutation in BBO 209
6.4.2 Experiments and Results 211
6.5 The Difference Mean Based Harmony Search Algorithm 214
6.5.1 Difference Mean Based Perturbation (DMP) Method 214
6.5.2 The DMP-HS Algorithm 214
6.5.3 Simulation Results 215
6.6 Summary 218
7 Hybrid Metaheuristic Approach for Protein Structure Prediction 221
7.1 Introduction 221
7.2 The Hybridization Framework 222
7.2.1 Improved PSO (IPSO) 223
7.2.2 Improved DE (IDE) 224
7.2.3 The HPSODE Algorithm 224
7.3 Experiments for PSP Problem 226
7.3.1 Simulation Strategy 226
7.3.2 Results and Discussion 228
7.4 Summary 229
8 Conclusions and Future Research 231
8.1 Discussions 231
8.2 Future Research Directions 233
Appendix References 234
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version: 1.4 234

Erscheint lt. Verlag 5.3.2018
Reihe/Serie Emergence, Complexity and Computation
Emergence, Complexity and Computation
Zusatzinfo XXIX, 220 p. 59 illus., 54 illus. in color.
Verlagsort Cham
Sprache englisch
Themenwelt Informatik ► Theorie / Studium ► Künstliche Intelligenz / Robotik
Naturwissenschaften ► Biologie
Technik
Schlagworte AB off-lattice Model • Complexity • Fitness Landscape Analysis • Metaheuristic Algorithms • Protein Structure • Protein Structure Prediction • PSP
ISBN-10 3-319-74775-4 / 3319747754
ISBN-13 978-3-319-74775-0 / 9783319747750
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