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SCOP: A Structural Classification of Proteins Database

SCOP: A Structural Classification of Proteins Database. Loredana Lo Conte, Bart Ailey and Cyrus Chothia Nucleic Acids Research, Vol. 28, No. 1, pp. 257– 259, 2000 Date: Aug. 19, 2005 Created by Jing-Liang Hsin. Abstract.

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SCOP: A Structural Classification of Proteins Database

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  1. SCOP: A Structural Classification of Proteins Database Loredana Lo Conte, Bart Ailey and Cyrus Chothia Nucleic Acids Research, Vol. 28, No. 1, pp. 257– 259, 2000 Date: Aug. 19, 2005 Created by Jing-Liang Hsin

  2. Abstract The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known Protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and distant evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database so far. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop.mrc-lmb. cam.ac.uk/scop/

  3. Classification • Family • All proteins that have residue identities of 30% and greater. • The proteins that have lower sequence identities but whose functions and structures are very similar. • Superfamily • Families whose proteins have low sequence identities but whose structures and, in many cases, functional features suggest that a common evolutionary origin is probable. • Common fold • Superfamilies and families are defined as having a common fold if their proteins have the same major secondary structures in the same arrangement and with the same topological connections.

  4. Classification • Class • all-α：those whose structure is essentially formed by α-helices • all-β：those whose structure is essentially formed by β -sheets • α/β： those with α-helices and β-strands • α+β：mainly antiparallel beta sheets (segregated alpha and beta regions) • multi-domain：those with domains of different fold and for which no homologues are known at present.

  5. Website • SCOP

  6. Reference • Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540. [PDF] • Lo Conte L., Brenner S. E., Hubbard T.J.P., Chothia C., Murzin A. (2002). SCOP database in 2002: refinements accommodate structural genomics. Nucl. Acid Res. 30(1), 264-267. [PDF] • Andreeva A., Howorth D., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin A.G. (2004). SCOP database in 2004: refinements integrate structure and sequence family data. Nucl. Acid Res. 32:D226-D229. [PDF].

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