Chemical Theory and Multiscale Simulation in Biomolecules: From Principles to Case Studies helps readers understand what simulation is, what information modeling of biomolecules can provide, and how to compare this information with experiments. Beginning with an introduction to computational theory for modeling, the book goes on to describe how to control the conditions of modeling systems and possible strategies for time-cost savings in computation. Part Two further outlines key methods, with step-by-step guidance supporting readers in studying and practicing simulation processes. Part Three then shows how these theories are controlled and applied in practice, through examples and case studies on varied applications.
This book is a practical guide for new learners, supporting them in learning and applying molecular modeling in practice, whilst also providing more experienced readers with the knowledge needed to gain a deep understanding of the theoretical background behind key methods.
1. Chapter 1 Introduction to biomolecular simulations - p. 1 2. Chapter 2 Molecular mechanics and force field - p. 13 3. Chapter 3 Quantum chemistry theory - p. 31 4. Chapter 4 Machine learning - p. 51 5. Chapter 5 Monte Carlo and molecular dynamics - p. 83 6. Chapter 6 Control and adjustment of simulation conditions - p. 99 7. Chapter 7 Multiscale model - p. 119 8. Chapter 8 Enhanced sampling - p. 141 9. Chapter 9 Software and hardware - p. 167 10. Chapter 10 Protein folding - p. 191 11. Chapter 11 RNA folding and structure prediction - p. 207 12. Chapter 12 Enzyme catalysis - p. 227 13. Chapter 13 Post-translational modification of proteins - p. 243 14. Chapter 14 Regulation of small molecule on proteins - p. 255 15. Chapter 15 Recognition of protein with nucleic acid - p. 273 16. Chapter 16 Dynamics and functions of membrane proteins - p. 287 17. Chapter 17 Assembly and functions of complex of multiple components - p. 307 18. Chapter 18 Protein small molecule design - p. 323 19. Chapter 19 Molecule scale - p. 341 20. References - p. 346 21. Chapter 20 System scale - p. 351 22. Index - p. 363
Chemical Theory and Multiscale Simulation in Biomolecules: From Principles to Case Studies helps readers understand what simulation is, what information modeling of biomolecules can provide, and how to compare this information with experiments. Beginning with an introduction to computational theory for modeling, the book goes on to describe how to control the conditions of modeling systems and possible strategies for time-cost savings in computation. Part Two further outlines key methods, with step-by-step guidance supporting readers in studying and practicing simulation processes. Part Three then shows how these theories are controlled and applied in practice, through examples and case studies on varied applications.
This book is a practical guide for new learners, supporting them in learning and applying molecular modeling in practice, whilst also providing more experienced readers with the knowledge needed to gain a deep understanding of the theoretical background behind key methods.
1. Chapter 1 Introduction to biomolecular simulations - p. 1 2. Chapter 2 Molecular mechanics and force field - p. 13 3. Chapter 3 Quantum chemistry theory - p. 31 4. Chapter 4 Machine learning - p. 51 5. Chapter 5 Monte Carlo and molecular dynamics - p. 83 6. Chapter 6 Control and adjustment of simulation conditions - p. 99 7. Chapter 7 Multiscale model - p. 119 8. Chapter 8 Enhanced sampling - p. 141 9. Chapter 9 Software and hardware - p. 167 10. Chapter 10 Protein folding - p. 191 11. Chapter 11 RNA folding and structure prediction - p. 207 12. Chapter 12 Enzyme catalysis - p. 227 13. Chapter 13 Post-translational modification of proteins - p. 243 14. Chapter 14 Regulation of small molecule on proteins - p. 255 15. Chapter 15 Recognition of protein with nucleic acid - p. 273 16. Chapter 16 Dynamics and functions of membrane proteins - p. 287 17. Chapter 17 Assembly and functions of complex of multiple components - p. 307 18. Chapter 18 Protein small molecule design - p. 323 19. Chapter 19 Molecule scale - p. 341 20. References - p. 346 21. Chapter 20 System scale - p. 351 22. Index - p. 363
