SCOPe Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Three proposals to the NIH for continued funding have been unsuccessful. If our current NIH proposal is not funded, SCOPe will shut down permanently in Summer 2017 as Dr. Chandonia will need to seek a new position.

Main References

All 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].
Newer features of SCOPe are described in:
  1. Chandonia JM, Fox NK, Brenner SE. 2017. SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins—extended Database. Journal of Molecular Biology. Available online 30 November 2016, ISSN 0022-2836. doi:0.1016/j.jmb.2016.11.023. [PDF].
Users of SCOP (version 1) releases should cite:
  1. 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].

Additional References

This paper discusses the principles behind SCOP and how to use it:
  1. 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].
This paper discusses how people have used SCOP and SCOPe in recent years:
  1. Fox NK, Brenner SE, Chandonia JM. 2015. The value of protein structure classification information—surveying the scientific literature. Proteins. doi: 10.1002/prot.24915. [PDF].
Further development of SCOP is described in:
  1. 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],
  2. 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
  3. 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:
  1. 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],
  2. 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
  3. 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:
  1. Chandonia JM, Brenner SE. 2006. The impact of structural genomics: expectations and outcomes. Science 311:347-51. [PDF]|[Supplementary Info].
Older SCOP references:
  1. Hubbard TJP, Murzin AG, Brenner SE, Chothia C. 1997. SCOP: a structural classification of proteins database. Nucleic Acids Research 25:236-239. [PDF],
  2. 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],
  3. 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
  4. 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].