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.
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.
Improvements in automation have allowed us to classify over 11,000 new PDB structures into the SCOP 1.75 hierarchy, to produce SCOPe 2.01 (see the Online help for details). We have taken a very conservative approach to using automation to classify new structures: only full-length chains that could be confidently matched to existing, manually curated SCOP domains in the first 7 SCOP classes were added to this release. We are continuing to benchmark our automated classification methods against prior versions of SCOP, to be sure the results of automation are completely consistent with manual curation. In addition, we manually corrected several SCOP bugs in this release—click on the Stats & History menu for details.
Improvements to the current website, as well as automated classification, are made possibly by an improved infrastructure underlying the database. New features include a new, integrated web interface (which is still being developed and improved), and a SQL back end (click the Downloads menu to obtain a copy).
SCOPe 2.01 was previously released to the public as SCOP 1.75A. No data have been harmed (or changed) in renaming the database.
All data in SCOPe (including the data from older releases of SCOP and Astral) are freely available to all users.
There are several alternative pronunciations of the vowels in the word SCOPe. All are considered correct.