SCOPe 2.08 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.
Sequences and subsets for SCOPe 2.08-stable are still being generated, and will be available soon.

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 page.

SCOPe parseable files for stable release 2.08:

Parseable files for previous stable releases of SCOP and SCOPe :

Astral data

The Astral 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.

Offsite archive

The SCOPe parseable files for all stable releases, along with the corresponding MySQL database and all ASTRAL sequences, are archived at Zenodo:

Free Software

  • Past (PDB Archival Snapshot Toolkit): Perl tools to efficiently store and archive multiple datestamped snapshots of the PDB.
    Version 1.42, released 29 July 2021, is needed to mirror the "PDB format-like file" bundles for large PDB structures, and includes a fix to the PDB's search URL.
  • XML2RAF: 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 StrBio Java class libraries.
    As of Astral 1.73, this software has been deprecated and replaced by XML2RAF.

Parseable files for very old releases of SCOP (without stable identifiers):

Old sequence libraries
  • Brenner S. E., Chothia C., Hubbard T. (1998)
    Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci. USA 95, 6073-6078. sdqib40-1.35.seg.fa, sdqib90-1.35.seg.fa
  • Park, S., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T. and Chothia, C. (1998)
    Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol. 284 (4), 1201-1210. PDB40D-J
  • 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, 14658-14663. PDB95D-T