SCOPe: Structural Classification of Proteins — extended. Release 2.04 (July 2014, new entries added 2014-11-15)
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References

Users should cite:
[1] Fox NK, Brenner SE, Chandonia JM. 2014. SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Research 42:D304-309. doi: 10.1093/nar/gkt1240. [PDF].

Users of SCOP (version 1) releases should cite:
[2] Murzin AG, Brenner SE, Hubbard TJP, Chothia C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 247:536-540. [PDF].


A discussion of how to use SCOP is in:
[3] Brenner SE, Chothia C, Hubbard TJP, Murzin AG. 1996. Understanding protein structure: Using SCOP for fold interpretation. Chap. 37 in: Doolittle RF, ed. Computer Methods for Macromolecular Sequence Analysis. Methods in Enzymology. Vol. 266. Orlando, FL: Academic Press. 635-643. [PDF].

More recent changes to SCOP are described in:
[4] Lo Conte L, Brenner SE, Hubbard TJP, Chothia C, Murzin AG. 2002. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Research 30: 264-267. [PDF],

[5] Andreeva A, Howorth D, Brenner SE, Hubbard TJP, Chothia C, Murzin AG. 2004. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Research 32:D226-D229. [PDF], and

[6] Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJP, Chothia C, Murzin AG. 2008. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Research 36:D419-425. [PDF].

Additional documentation about the ASTRAL sequences and subsets is in:
[7] Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. 2004. The ASTRAL compendium in 2004. Nucleic Acids Research 32:D189-D192. [PDF],

[8] Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. 2002. ASTRAL compendium enhancements. Nucleic Acids Research 30:260-263. [PDF], and

[9] Brenner SE, Koehl P, Levitt M. 2000. The ASTRAL compendium for sequence and structure analysis. Nucleic Acids Research 28:254-256. [PDF]

A description of the trends in SCOP classification of newly solved protein structures is in:
[10] Chandonia JM, Brenner SE. 2006. The impact of structural genomics: expectations and outcomes. Science 311:347-51. [PDF]|[Supplementary Info].

Older SCOP references:
[11] Hubbard TJP, Murzin AG, Brenner SE, Chothia C. 1997. SCOP: a structural classification of proteins database. Nucleic Acids Research 25:236-239. [PDF],

[12] Hubbard TJP, Ailey B, Brenner SE, Murzin AG, Chothia C. 1998. SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallographica D54:1147-1154. [PDF],

[13] Hubbard TJP, Ailey B, Brenner SE, Murzin AG, Chothia C. 1999. SCOP: a structural classification of proteins database. Nucleic Acids Research 27:254-256. [PDF], and

[14] Lo Conte L, Ailey B, Hubbard TJP, Brenner SE, Murzin AG, Chothia C. 2000. SCOP: a structural classification of proteins database. Nucleic Acids Research 28:257-259. [PDF].


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