SCOPe 2.04 data
Starting with SCOPe version 2.01, data from all versions of
SCOPe, SCOP, and Astral since 1.55 are stored
in a relational database.
To download a copy of the MySQL database released with stable
2.04 (sql.bz2 format),
click here (740.4 MB)
Documentation for our schema is available
(ER diagrams were autogenerated using
Note that we have removed the astral_seq_blast*
tables from the download, since these tables are so
large. They are available on request.
Since SCOP release 1.55, the
SCOP classification has
been distributed in the form of a
set of sequences, coordinates, and parseable files, all based on a
new set of identifiers.
For an account of these changes, file
formats, file contents and meaning, see the Lo Conte et al (2002)
and Chandonia et al (2004) references on the
Help > References
SCOPe parseable files for stable release 2.04:
for access to the parseable files and MySQL database released with the periodic update to SCOPe
2.04 on 2014-12-18
Parseable files for previous stable releases of SCOP
- dir.des.scop(e).txt: 2.03, 2.02, 2.01, 1.75, 1.73, 1.71, 1.69, 1.67, 1.65, 1.63, 1.61, 1.59, 1.57, 1.55
- dir.cla.scop(e).txt: 2.03, 2.02, 2.01, 1.75, 1.73, 1.71, 1.69, 1.67, 1.65, 1.63, 1.61, 1.59, 1.57, 1.55
- dir.hie.scop(e).txt: 2.03, 2.02, 2.01, 1.75, 1.73, 1.71, 1.69, 1.67, 1.65, 1.63, 1.61, 1.59, 1.57, 1.55
- dir.com.scop(e).txt: 2.03, 2.02, 2.01, 1.75, 1.73, 1.71, 1.69, 1.67, 1.65, 1.63
compendium is a collection of software and databases, partially
derived from SCOP(e), that aid research
into protein structure and evolution. These data are available on the
Downloads > Astral Sequences & Subsets page.
The SCOPe parseable files for all stable releases,
along with the corresponding MySQL database and all
ASTRAL sequences, are
archived at Zenodo:
(PDB Archival Snapshot Toolkit):
Perl tools to efficiently store and archive multiple datestamped
snapshots of the PDB.
Version 1.4, released 22 January 2015, is needed to mirror
the "PDB format-like file" bundles for large PDB structures.
Perl software to create RAF maps
from PDB XML files, used to build
Astral 1.73 and above.
Version 1.02, released 22 January 2015, ignores incorrectly
formatted PDB entries with multi-letter chain identifiers.
MakeRAF: Java software to create
RAF maps from
PDB files is
included in the
As of Astral 1.73,
this software has been deprecated and replaced by
Parseable files for very old releases of
(without stable identifiers):
Old sequence libraries
Brenner S. E., Chothia C., Hubbard T. (1998)
sequence comparison methods with reliable structurally
identified distant evolutionary relationships. Proc. Natl.
Acad. Sci. USA 95, 6073-6078.
Park, S., Karplus, K., Barrett, C., Hughey, R., Haussler, D.,
Hubbard, T. and Chothia, C. (1998)
using multiple sequences detect three times as many remote
homologues as pairwise methods. J. Mol. Biol. 284 (4),
Teichmann, S. A., Park, J. and Chothia, C. (1998)
Structural assignments to the Mycoplasma genitalium
proteins show extensive gene duplications and domain
rearrangements. Proc. Natl. Acad. Sci USA 95,