37] Understanding protein structure: Using scop for fold interpretation

Abstract

The structure of a protein can elucidate its function, in both general and specific terms, and its evolutionary history. Extracting this information, however, requires the knowledge of the structure and its relationships with other proteins. These two aspects are not independent, for an understanding of the structure of a single protein requires a general knowledge of the folds that proteins adopt while an understanding of relationships requires detailed information about the structures of many proteins. The structural classification of protein (scop) database is organized on a number of hierarchical levels, with the principal ones being family, superfamily, fold, and class. Within the hierarchy, the unit of categorization is the protein domain rather than whole proteins, because protein domains are typically the units of protein evolution, structure, and function. Thus, different regions of a single protein may appear in multiple places in the scop hierarchy under different folds or, in the case of repeated domains, several times under the same fold. Computational approaches are now beginning to play an important role in the understanding of protein structures and can be fruitfully used in conjunction with the scop classification.