Volume Two of this two volume sequence focuses on protein structure prediction and includes protein threading, De novo methods, applications to membrane proteins and protein complexes, structure-based drug design, as well as structure prediction as a systems problem. A series of appendices review the biological and chemical basics related to protein structure, computer science for structural informatics, and prerequisite mathematics and statistics. This volume presents a comprehensive overview of protein structure prediction methods. Each chapter is a self contained review. The coverage includes: De novo methods of protein structure prediction; applications to membrane proteins and protein complexes; and more. This is the 2'nd volume of a two-volume sequence.