Abstract
Structural Classification of Proteins—extended (SCOPe, http://scop.berkeley.edu) is a database of protein structural relationships that extends the SCOP database. SCOP is a manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. Development of the SCOP 1.x series concluded with SCOP 1.75. The ASTRAL compendium provides several databases and tools to aid in the analysis of the protein structures classified in SCOP, particularly through the use of their sequences. SCOPe extends version 1.75 of the SCOP database, using automated curation methods to classify many structures released since SCOP 1.75. We have rigorously benchmarked our automated methods to ensure that they are as accurate as manual curation, though there are many proteins to which our methods cannot be applied. SCOPe is also partially manually curated to correct some errors in SCOP. SCOPe aims to be backward compatible with SCOP, providing the same parseable files and a history of changes between all stable SCOP and SCOPe releases. SCOPe also incorporates and updates the ASTRAL database. The latest release of SCOPe, 2.03, contains 59 514 Protein Data Bank (PDB) entries, increasing the number of structures classified in SCOP by 55% and including more than 65% of the protein structures in the PDB.
Highlights
Most proteins have structural similarities with other proteins and, in many of these cases, share a common evolutionary origin
The hierarchy of Structural Classification of Proteins (SCOP) domains comprises the following levels: ‘Species’ representing a distinct protein sequence and its naturally occurring or artificially created variants; ‘Protein’ grouping together similar sequences of essentially the same functions that either originate from different biological species or represent different isoforms within the same species; ‘Family’ containing proteins with similar sequences but typically distinct functions and ‘Superfamily’ bridging together protein families with common functional and structural features inferred to be from a common evolutionary ancestor
Over the course of benchmarking our new method, we found the method would have been able to automatically assign domains for approximately half of the Protein Data Bank (PDB) entries that were manually curated in prior versions of SCOP, with no substantial differences (i.e. >10 residue difference in any domain boundary) between the automatically assigned and manually curated domain boundaries
Summary
Most proteins have structural similarities with other proteins and, in many of these cases, share a common evolutionary origin. We describe SCOP—extended (SCOPe), a database that extends SCOP 1.75, with the aim of providing ongoing classification of new PDB structures in the context of the SCOP hierarchy, backward compatibility with SCOP, manual correction of errors and stable releases suitable for benchmarking. We have developed new methods for automatically classifying structures similar to those already in SCOP, and we have benchmarked it rigorously with the goal of achieving accuracy comparable to fully hand-curated SCOP releases (i.e. through SCOP 1.71).
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