Fundamentals of Molecular Structural Biology, Second Edition reviews the mathematical and physical foundations of molecular structural biology, covering the latest advancements. The book begins with historical perspectives before exploring mathematical concepts, physical aspects of chemistry, the chemical basis of biology, structural analysis, visualization, protein folding, transcription, RNA processing, cell signaling, and computational molecular biology. Additionally, this new edition delves into AI fundamentals and applications, including AlphaFold and RoseTTAFold. This fully updated edition provides a detailed overview of the fundamental concepts across molecular structural biology and acts as an ideal guide for researchers and advanced students.
Given the increasingly interdisciplinary nature of this subject, this book provides early career researchers and those shifting into an adjacent field a "fundamentals" resource to get them up-to-speed on the foundations of a particular field.
1. Chapter 1. Introduction—a historical perspective - p. 1 2. Chapter 2. Mathematical preliminaries - p. 13 3. 2.1 Measurements: standards and units - p. 13 4. 2.1.1 Functions - p. 15 5. 2.1.2 Vectors - p. 22 6. 2.1.2.1 Concept of vector in physics - p. 22 7. 2.1.2.2 Vector as an ordered set of numbers - p. 24 8. 2.1.2.3 Mathematical viewpoint of vector - p. 27 9. 2.1.3 Matrices and determinants - p. 28 10. 2.1.3.1 Systems of linear equations - p. 28 11. 2.1.3.2 Matrices - p. 30 12. 2.1.3.3 Determinants - p. 33 13. 2.1.4 Calculus - p. 34 14. 2.1.4.1 Differentiation - p. 34 15. 2.1.4.2 Integration - p. 37 16. 2.1.4.3 Multivariate function - p. 40 17. 2.1.4.4 Vector operators - p. 42 18. 2.1.4.5 Applications - p. 43 19. 2.1.5 Series and limits - p. 44 20. 2.1.6 Integral transform - p. 47 21. 2.2 Sample questions - p. 49 22. Chapter 3. Physical basis of chemistry - p. 53 23. 3.1 Classical mechanics - p. 53 24. 3.2 Kinetic theory of gases - p. 63 25. 3.3 Thermodynamics - p. 64 26. 3.4 Electricity and magnetism - p. 65 27. 3.4.1 Electric field - p. 65 28. 3.4.2 Electric potential - p. 68 29. 3.4.3 Magnetic field - p. 69 30. 3.4.4 Electromagnetic wave - p. 69 31. 3.4.5 Interference of light waves - p. 71 32. 3.4.6 Scattering of electromagnetic waves - p. 73 33. 3.5 Quantum physics - p. 74 34. 3.6 Some elements of statistics - p. 84 35. Sample questions - p. 87 36. Chapter 4. Chemical basis of biology - p. 91 37. Chapter 5. Biomacromolecules - p. 115 38. Chapter 6. Structure analysis and visualization - p. 151 39. 6.1 X-ray crystallography - p. 151 40. 6.1.1 Scattering of X-rays by an atom - p. 152 41. 6.1.2 Diffraction from a crystal – Laue equations - p. 156 42. 6.1.3 Diffraction and Fourier transform - p. 160 43. 6.1.4 Convolution and diffraction - p. 161 44. 6.1.5 The electron density equation - p. 162 45. 6.1.5.1 Phase problem and the Patterson function - p. 163 46. 6.1.5.2 Isomorphous replacement - p. 164 47. 6.1.5.3 Electron density sharpening - p. 164 48. 6.1.6 Refinement - p. 165 49. 6.2 Nuclear magnetic resonance (NMR) - p. 166 50. 6.3 Cryo-electron microscopy - p. 170 51. 6.4 Representation of structures - p. 179 52. Sample questions - p. 188 53. Chapter 7. Protein folding - p. 191 54. Chapter 8. DNA synthesis: Replication - p. 215 55. Chapter 9. Transcription - p. 277 56. Chapter 10. RNA processing - p. 337 57. Chapter 11. Translation - p. 369 58. Chapter 12. DNA damage and repair - p. 431 59. Chapter 13. Recombination - p. 461 60. Chapter 14. Membrane structure and function - p. 493 61. Chapter 15. Fundamentals of structural genomics - p. 515 62. Chapter 16. Cell signaling and systems biology - p. 531 63. Chapter 17. Macromolecular assemblies - p. 557 64. Chapter 18. Computational molecular biology - p. 575 65. Chapter 19. Artificial intelligence (AI) applications - p. 601 66. Index - p. 635
Fundamentals of Molecular Structural Biology, Second Edition reviews the mathematical and physical foundations of molecular structural biology, covering the latest advancements. The book begins with historical perspectives before exploring mathematical concepts, physical aspects of chemistry, the chemical basis of biology, structural analysis, visualization, protein folding, transcription, RNA processing, cell signaling, and computational molecular biology. Additionally, this new edition delves into AI fundamentals and applications, including AlphaFold and RoseTTAFold. This fully updated edition provides a detailed overview of the fundamental concepts across molecular structural biology and acts as an ideal guide for researchers and advanced students.
Given the increasingly interdisciplinary nature of this subject, this book provides early career researchers and those shifting into an adjacent field a "fundamentals" resource to get them up-to-speed on the foundations of a particular field.
1. Chapter 1. Introduction—a historical perspective - p. 1 2. Chapter 2. Mathematical preliminaries - p. 13 3. 2.1 Measurements: standards and units - p. 13 4. 2.1.1 Functions - p. 15 5. 2.1.2 Vectors - p. 22 6. 2.1.2.1 Concept of vector in physics - p. 22 7. 2.1.2.2 Vector as an ordered set of numbers - p. 24 8. 2.1.2.3 Mathematical viewpoint of vector - p. 27 9. 2.1.3 Matrices and determinants - p. 28 10. 2.1.3.1 Systems of linear equations - p. 28 11. 2.1.3.2 Matrices - p. 30 12. 2.1.3.3 Determinants - p. 33 13. 2.1.4 Calculus - p. 34 14. 2.1.4.1 Differentiation - p. 34 15. 2.1.4.2 Integration - p. 37 16. 2.1.4.3 Multivariate function - p. 40 17. 2.1.4.4 Vector operators - p. 42 18. 2.1.4.5 Applications - p. 43 19. 2.1.5 Series and limits - p. 44 20. 2.1.6 Integral transform - p. 47 21. 2.2 Sample questions - p. 49 22. Chapter 3. Physical basis of chemistry - p. 53 23. 3.1 Classical mechanics - p. 53 24. 3.2 Kinetic theory of gases - p. 63 25. 3.3 Thermodynamics - p. 64 26. 3.4 Electricity and magnetism - p. 65 27. 3.4.1 Electric field - p. 65 28. 3.4.2 Electric potential - p. 68 29. 3.4.3 Magnetic field - p. 69 30. 3.4.4 Electromagnetic wave - p. 69 31. 3.4.5 Interference of light waves - p. 71 32. 3.4.6 Scattering of electromagnetic waves - p. 73 33. 3.5 Quantum physics - p. 74 34. 3.6 Some elements of statistics - p. 84 35. Sample questions - p. 87 36. Chapter 4. Chemical basis of biology - p. 91 37. Chapter 5. Biomacromolecules - p. 115 38. Chapter 6. Structure analysis and visualization - p. 151 39. 6.1 X-ray crystallography - p. 151 40. 6.1.1 Scattering of X-rays by an atom - p. 152 41. 6.1.2 Diffraction from a crystal – Laue equations - p. 156 42. 6.1.3 Diffraction and Fourier transform - p. 160 43. 6.1.4 Convolution and diffraction - p. 161 44. 6.1.5 The electron density equation - p. 162 45. 6.1.5.1 Phase problem and the Patterson function - p. 163 46. 6.1.5.2 Isomorphous replacement - p. 164 47. 6.1.5.3 Electron density sharpening - p. 164 48. 6.1.6 Refinement - p. 165 49. 6.2 Nuclear magnetic resonance (NMR) - p. 166 50. 6.3 Cryo-electron microscopy - p. 170 51. 6.4 Representation of structures - p. 179 52. Sample questions - p. 188 53. Chapter 7. Protein folding - p. 191 54. Chapter 8. DNA synthesis: Replication - p. 215 55. Chapter 9. Transcription - p. 277 56. Chapter 10. RNA processing - p. 337 57. Chapter 11. Translation - p. 369 58. Chapter 12. DNA damage and repair - p. 431 59. Chapter 13. Recombination - p. 461 60. Chapter 14. Membrane structure and function - p. 493 61. Chapter 15. Fundamentals of structural genomics - p. 515 62. Chapter 16. Cell signaling and systems biology - p. 531 63. Chapter 17. Macromolecular assemblies - p. 557 64. Chapter 18. Computational molecular biology - p. 575 65. Chapter 19. Artificial intelligence (AI) applications - p. 601 66. Index - p. 635
