Molecular dynamics is an important technique with applications in many areas, including drug design, protein engineering, macromolecular structure determination, and molecular recognition. This book concentrates on these exciting applications while briefly summarizing the essential mathematical background. Using standard molecular dynamics and related algorithms, results are presented on protein, carbohydrate, and nucleotide modeling and dynamics. Chapters covering relatively new applications, such as simulated annealing protocol and the free energy perturbation method, are also included. Molecular biologists, biochemists, and researchers in structural molecular biology, chemistry, crystallography, and computer modelling will find this book a useful reference resource.
Table of Contents
Simulating the Dynamics of Macromolecules (T. P. Flores and D. S. Moss). Conformational Variability of Insulin: A Molecular Dynamics Analysis (L.S.D. Caves, D. T. Nguyen, R. E. Hubbard). Molecular Dynamics Simulations of Carbohydrates (J. Kohler). Prediction of the Three-Dimensional Structures of Ribonucleic Acids from tRNA to 16S Ribosomal RNA (A. Malhotra, R. K. -Z Tan and S. C. Harvey). Refinement of the Three-Dimensional Structures of Proteins and Nucleic Acids (A. T. Brunger). Applications of Free Energy Calculations (M. A. Williams, M.A.S. Sagi and J. M. Goodfellow).