Molecular dynamics : applications in molecular biology

목차 (Table of Contents)

• CONTENTS
• Preface = ⅶ
• The Contributors = ⅷ
• 1. Simulating the dynamics of macromolecules / T. P. Flores ; D. S. Moss = 1
• Introduction = 1
• Molecular dynamics = 2
• Potential energy functions = 4
• Treatment of boundaries = 11
• Calculation of non-bonded interactions = 13
• Constrained dynamics = 14
• Constant temperature and pressure = 14
• Molecular dynamics simulations = 15
• Solution of NMR structures = 17
• Refinement of X-ray crystallographic data with molecular dynamics = 19
• Calculation of free energies of perturbation = 19
• Other methods employed in molecular simulations = 21
• 2. Conformational variability of insulin : a molecular dynamics analysis / L. S. D. Caves ; D. T. Nguyen ; R. E. Hubbard = 27
• Introduction = 27
• Materials and methods = 29
• General quality of the simulations = 36
• Atomic motion = 45
• Secondary structure motion = 52
• Interconformer relationships = 58
• Summary and conclusions = 62
• 3. Molecular dynamics simulations of carbohydrates / J. K$$\ddot{o}$$hler = 69
• Introduction = 69
• Notes on theoretical methods = 70
• Molecular dynamics calculations on cyclodextrins = 72
• Molecular dynamics simulation of crystalline α-cyclodextrin hexahydrate at 293 K = 74
• Molecular dynamics simulation of crystallin β-cyclodextrin dodecahydrate at 293 K and 120 K = 81
• Flip-flop hydrogen bonding = 88
• Conformational differences between α-cyclodextrin in aqueous solution and in aqueous solution and in crystalline form = 95
• Three-centre hydrogen bonds in cyclodextrins = 99
• 4. Prediction of the three-dimentsional structures of ribonucleic acids : from tRNA to 16S ribosomal RNA / A. Malhotra, R. K. -Z. Tan ; S. C. Harvey = 107
• Introduction = 107
• An automated RNA folding procedure = 111
• tRNA modelling : a test for the folding prcedure = 116
• Modelling ribosomal RNA : 16S RNA in the E. coli 30S subunit = 121
• Modelling results = 124
• Conclusions and discussion = 133
• 5. Refinement of three-dimensional structures of proteins and nucleic acids / A. T. Br$$\ddot{u}$$nger = 137
• Introduction = 137
• General methodology = 139
• Solution to NMR structure determination and refinements = 144
• Crystallographic refinement of macromolecules = 152
• Combined molecular replacement and Patterson refinement = 167
• Concluding remarks = 171
• 6. Application of free energy calculations / M. A. Williams ; M. A. S. Saqi ; J. M. Goodfellow = 179
• Introduction = 179
• Background = 180
• Theroy and computational procedures = 181
• Applications = 183
• Summary = 190
• Appendix 1 : energy, entropy and free energy = 191
• Index = 197