The homology modeling method is an important tool in protein engineering and drug design when an experimental 3D structure is not available. Development of distance geometry-based homology modeling offers a holistic approach to protein modeling thus expanding the scope of this method to protein threading and protein folding. This book is the first of its kind to give a complete account of the field including structural principles and sequence-to-structural relationships in the PDB. This book is intended for use by biologists and modelers who are new to homology modeling methods, and serves as a good starting point for further research.