Rapid methods for comparing protein structures and scanning structure datahases

Databases of three-dimensional macromolecular structures became so large that fast search tools and comparison methods were needed and were actually designed. All of them employ simplified representations of the three-dimensional structure: strings of characters of variable length, which can be handled with procedures that were designed for sequence analysis; fixed dimension arrays that can be processed with standard statistical methods; ensembles of secondary structural elements, which are much less numerous than the atoms/residues of the protein; and continuous representations of the backbone, through stereochemical figures. Some of these computational procedures were developed long ago, when computers were too slow, and others have been designed recently, with the specific aim of handling large amount of information. The present article is focused on the algorithms that allow fast structure comparison, particularly suitable to handle large databases, and should provide a comprehensive picture, useful for the development and the assessment of novel tools.