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.

Welcome to the SCOPe website!

SCOPe is a database developed at the Berkeley Lab and UC Berkeley that extends SCOP (version 1). SCOPe classifies many structures released since SCOP 1.75 through a combination of automation and manual curation, and corrects some errors, aiming to have the same accuracy as the fully hand-curated SCOP releases. SCOPe also incorporates and updates the Astral database.

In addition to new SCOPe releases, the SCOPe website provides integrated access to data found in all releases of the SCOP and Astral databases that feature stable identifiers (i.e., those since release 1.55). A history of all changes between consecutive releases of SCOP and SCOPe is available under the Stats & History menu.

In order to facilitate use of SCOPe data by SCOP and Astral users, we provide SCOPe data in parseable files in the same formats as the SCOP and Astral databases. SCOPe uses the same stable identifiers (e.g., sunid, sid, sccs) as were used for prior releases of SCOP and Astral.

Authors

  • The SCOPe authors are Naomi K. Fox, Steven E. Brenner, and John-Marc Chandonia.
  • The SCOP authors are Alexey G. Murzin, John-Marc Chandonia, Antonina Andreeva, Dave Howorth, Loredana Lo Conte, Bartlett G. Ailey, Steven E. Brenner, Tim J. P. Hubbard, and Cyrus Chothia.
  • The ASTRAL authors are John-Marc Chandonia, Naomi K. Fox, Degui Zhi, Gary Hon, Loredana Lo Conte, Nigel Walker, Patrice Koehl, Michael Levitt, and Steven E. Brenner.

Synopsis and News

Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.

The Astral compendium provides databases and tools useful for analyzing protein structures and their sequences. It is partially derived from, and augments SCOP(e). Most of the resources provided here depend upon the coordinate files maintained and distributed by the Protein Data Bank.

In SCOPe 2.06, we have continued to perform manual curation of new Folds, Superfamilies, and Families. We classified members of 65 Pfam families having the most structures (all those with at least 15 PDB entries) that had not previously had a classified representative in SCOP or SCOPe.

We have also moved cloning artifacts that we could identify (e.g., expression tags) to a new class (l: Artifacts) in order to separate them from the homology-based curations in the rest of the SCOPe hierarchy. Including such artifacts can result in similarity between non-homologous sequences. We separated 21,876 tags, with lengths ranging from 1 to 28 residues, from their original domains. Where possible, we kept the same sid and sunid identifiers for the trimmed domains. Note that not all tags are clearly annotated in the PDB, so we intend to improve our detection algorithm in future stable SCOPe releases. We also generated a new set of full-length Astral chain sequences based on PDB SEQRES records, with these tags removed, as well as nonredundant subsets of this set.

License

All data in SCOPe (including the data from older releases of SCOP and Astral) are freely available to all users.

Pronunciation

There are several alternative pronunciations of the vowels in the word SCOPe. All are considered correct.

Funding

This work is supported by the National Institutes of Health (R01-GM073109) through the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.