Structural Classification of Proteins database

The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins. Proteins with the same shapes but having little sequence or functional similarity are placed in different superfamilies, and are assumed to have only a very distant common ancestor. Proteins having the same shape and some similarity of sequence and/or function are placed in 'families', and are assumed to have a closer common ancestor. The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins. Proteins with the same shapes but having little sequence or functional similarity are placed in different superfamilies, and are assumed to have only a very distant common ancestor. Proteins having the same shape and some similarity of sequence and/or function are placed in 'families', and are assumed to have a closer common ancestor. The SCOP database is freely accessible on the internet. SCOP was created in 1994 in the Centre for Protein Engineering and the Laboratory of Molecular Biology. It was maintained by Alexey G. Murzin and his colleagues in the Centre for Protein Engineering until its closure in 2010 and subsequently at the Laboratory of Molecular Biology in Cambridge, England. Similar to CATH and Pfam databases, SCOP provides a classification of individual structural domains of proteins, rather than a classification of the entire proteins which may include a significant number of different domains. As of January 2014, the work on SCOP has been discontinued and the last official version of SCOP is 1.75 (released June 2009). Since then SCOPe from UC Berkeley has been responsible for updating the database in a compatible manner, with a combination of automated and manual methods. As of April 2019, the latest release is SCOPe 2.07 (March 2018). The prototype of a new Structural Classification of Proteins 2 (SCOP2) database from Cambridge has been made publicly available. SCOP2 replaces the SCOP hierarchy with a directed acyclic graph for more flexibility and retains its best features. It is incompatible with SCOP and is yet to be populated. The source of protein structures is the Protein Data Bank. The unit of classification of structure in SCOP is the protein domain. What the SCOP authors mean by 'domain' is suggested by their statement that small proteins and most medium-sized ones have just one domain, and by the observation that human hemoglobin, which has an α2β2 structure, is assigned two SCOP domains, one for the α and one for the β subunit. The shapes of domains are called 'folds' in SCOP. Domains belonging to the same fold have the same major secondary structures in the same arrangement with the same topological connections. 1195 folds are given in SCOP version 1.75. Short descriptions of each fold are given. For example, the 'globin-like' fold is described as core: 6 helices; folded leaf, partly opened. The fold to which a domain belongs is determined by inspection, rather than by software.