This book provides systematic technical expositions of the computational methods for all major aspects of protein structure analysis, prediction and modeling. The chapters have been designed to address comprehensively the main topics of the field. In addition, chapters will be connected seamlessly through a careful design of the overall structure of the book. Topics have been selected carefully so that the book would be useful to a broad readership, including students, postdoctoral fellows, professional practitioners, as well as bioinformatic experts who want to brush up topics related to their own research areas. The book can be used as a textbook for upper undergraduate-level or beginning graduate-level bioinformatics courses. To facilitate learning, four appendices describing the prerequisites for reading this book have been included, in (1) biology, (2) computer science, (3) physics and chemistry, and (4) mathematics and statistics. Each chapter in the book is a self-contained review of a specific subject, designed to cover the following material: (1) the problem definition and a historical perspective, (2) mathematical or computational formulation of the problem, (3) computational methods and algorithms, (4) performance results, (5) existing software packages, and (6) the strengths, pitfalls, challenges, and future research directions.