Preface
Ying Xu, Dong Xu, Jie Liang, and John Wooley

Chapter 1: Overview of protein structure prediction and historical perspective.
John Wooley and Yuzhen Ye

Chapter 2: Empirical Force Fields.
Alexander D. MacKerell, Jr.

Chapter 3: Empirical Potential Functions for Computational Studies of Proteins.
Xiang Li and Jie Liang

Chapter 4: Protein Structure Domain Partition.
Stella Veretnik and Ilya Shindyalov

Chapter 5: Protein Structure Comparison and Classification.
Orhan Camolu and Ambuj K. Singh

Chapter 6: Computation of protein geometry and applications
Jie Liang

Chapter 7: Local Structure Prediction of Proteins.
V. A. Simossis and J. Heringa

Chapter 8: Protein Contact Map Prediction.
Xin Yuan and Christopher Bystroff

Chapter 9: Modeling Protein Aggregate Assembly and Structure.
Jun-tao Guo, Carol K. Hall, Ying Xu and Ronald Wetzel

Chapter 10: Homology-based Structure Modeling.
Zhexin Xiang

Chapter 11: Modeling Protein Structures Based on Density Maps at Intermediate Resolutions.
Jianpeng Ma

Chapter 12: Protein Structure Prediction by Protein Threading.
Ying Xu, Zhijie Liu, Liming Cai and Dong Xu

Chapter 13: De novo Protein Structure Prediction.
Ling-Hong Hung, Shing-Chung Ngan and Ram Samudrala

Chapter 14: Structure Prediction of Membrane Proteins.
Xiche Hu

Chapter 15: Structure Prediction of Protein Complexes
Brian Pierce and Zhiping Weng

Chapter 16: Structure-based Drug Design.
Kunbin Qu and Natasja Brooijmans

Chapter 17: Protein Structure Prediction as a Systems Problem.
Dong Xu and Ying Xu

Chapter 18: Resources and Infrastructure for Structural Bioinformatics.
Dong Xu, Jie Liang and Ying Xu

Appendix I: Biological Basics Related to Protein Structures.
Hong Guo and Haobo Guo

Appendix II: Computer Science for Structural Bioinformatics.
Guohui Lin, Dong Xu and Ying Xu

Appendix III: Physical and Chemical Basis for Structural Bioinformatics.
Hui Lu, Ognjen Perisic and Dong Xu

Appendix IV: Mathematics and Statistics for Studying Protein Structures.
Yang Dai and Jie Liang