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