Some of the derived databases focus on organizing proteins into groups according to similarities in their secondary structures.
The Distance Matrix Alignment (Dali) Fold Classification Database (Holm and Sander, 1994, 1996) provides a mapping of similarity of folding patterns from the PDB, organizing the known proteins into a tree of fold families. The Dali search engine keeps the database updated and is available to use to compare a probe structure to the PDB (Dali web page).
The Structure Classification of Proteins (SCOP) Database (Murzin et al., 1995; Conte et al., 2002) uses the PDB structural data to classify fold families of proteins and tries to illuminate evolutionary relationships. 'Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification' (SCOP web page).
The Class, Architecture, Topology and Homologous superfamily (CATH) Database (Orengo et al., 1997; Pearl et al., 2000) classifies protein structures by a combination of automatic and manual techniques. 'Class, derived from secondary structure content, is assigned for more than 90% of protein structures automatically. Architecture, which describes the gross orientation of secondary structures, independent of connectivities, is currently assigned manually. The topology level clusters structures according to their toplogical connections and numbers of secondary structures. The homologous superfamilies cluster proteins with highly similar structures and functions. The assignments of structures to toplogy families and homologous super-families are made by sequence and structure comparisons' (CATH web page).
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