Protein Structure Classification

The molecular basis of life rests on the activity of large biological macromolecules, including nucleic acids (DNA and RNA), carbohydrates, lipids, and proteins. Although each plays an essential role in life, there is something special about proteins, as they are the lead performers of cellular functions. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of these bio-molecules. This branch of biology has recently experienced a major uplift through the development of high-throughput structural studies aimed at developing a comprehensive view of the protein structure universe. Although these studies are generating a wealth of information that are stored into protein structure databases, the key to their success lies in our ability to organize and analyze the information contained in those databases, and to integrate that information with other efforts aimed at solving the mysteries behind cell functions. In this survey, the first step behind any such organization scheme, namely the classification of protein structures, is described. The properties of protein structures, with special attention to their geometry, are reviewed. Computer methods for the automatic comparison and classification of these structures are then reviewed along with the existing classifications of protein structures and their applications in biology, with a special focus on computational biology. The chapter concludes the review with a discussion of the future of these classifications.