The revised lectures presented in this volume are based on a course given by leading scholars at the C.I.M.E. Summer School held in Martina Franca, Italy, in July 2000. The 11 revised chapters presented were carefully revised and cross-reviewed in order to provide competent coverage of mathematical methods for protein structure analysis and design. The topics addressed pinpoint major issues arising in the development and analysis of models, algorithms, and software tools devoted to the structure of proteins, all of which play crucial roles in structural genomics and proteomics.