Abstract
The Structural Classification of Proteins (SCOP) database is a classification of protein domains organised according to their evolutionary and structural relationships. We report a major effort to increase the coverage of structural data, aiming to provide classification of almost all domain superfamilies with representatives in the PDB. We have also improved the database schema, provided a new API and modernised the web interface. This is by far the most significant update in coverage since SCOP 1.75 and builds on the advances in schema from the SCOP 2 prototype. The database is accessible from http://scop.mrc-lmb.cam.ac.uk.
Highlights
The Structural Classification of Proteins (SCOP) database is a classification that organises proteins of known three-dimensional structure according to their structural and evolutionary relationships [1]
In addition to HMM 1.75 models, the HMM 2.0 library contained models built from the domain sequences taken from other structural classification databases such as SCOPe [14], CATH [15] and ECOD [16] as well as from the entire protein chain sequences taken from the PDB
The development of SCOP has been always guided by its users feedback and needs
Summary
The SCOP database is a classification that organises proteins of known three-dimensional structure according to their structural and evolutionary relationships [1]. The classification levels currently organise more than 40 000 non-redundant domains that represent nearly 500 000 protein structures. As these relationships can sometimes span structural regions of different size, we provide domain boundaries for both, family and superfamily levels.
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