The axiom that structure determines function, and may therefore be used to predict function, lies at the heart of the structure prediction and structure-based function annotation areas covered in this book. Although it is the deluge of Structural Genomics outputs, many of unknown function, which has stimulated development of structure-based function prediction methods, all the methods can be applied, at least to some extent, to model structures. The first chapters of this book therefore cover generation and inference of structures for protein sequences. They are followed by discussions of the various ways in which knowledge of structure leads to function prediction, and finally by two chapters focusing on real-world applications to Structural Genomics outputs or protein models.