Years of research in biology have established that all cellular functions are deeply connected to the shape of their molecular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of 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. While these studies are generating a wealth of information, stored into protein structure databases, the key to their success lies in our ability to organize and analyze the information contained in these databases, and integrate it with other biological efforts aimed at solving the mysteries behind cell functions. In this survey, I focus on the first step behind any such organization scheme, namely the classification of protein structures. I review the properties of protein structures, with a special interest on their geometry. Computer methods for the automatic comparison and classification of these structures are then reviewed. In parallel, I describe the existing classifications of protein structures, and their applications in biology, with a special focus on computational biology. I conclude the review with a discussion on the future of these classifications.