SCOPe 2.06 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 SCOPe 2.06 (sql.bz2 format), click here (1.3 GB).
Documentation for our schema is available here. (ER diagrams were autogenerated using SchemaSpy.)
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 page.

SCOPe parseable files for stable release 2.06:

Click here for access to the parseable files and MySQL database released with the periodic update to SCOPe 2.06 on 2016-05-26.

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.

Free Software

  • Past (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.
  • 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