SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database

Abstract

SCOPe (Structural Classification of Proteins-extended, http://scop.berkeley.edu) is a database of relationships between protein structures that extends the Structural Classification of Proteins (SCOP) database. SCOP is an expert-curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. SCOPe classifies the majority of protein structures released since SCOP development concluded in 2009, using a combination of manual curation and highly precise automated tools, aiming to have the same accuracy as fully hand-curated SCOP releases. SCOPe also incorporates and updates the ASTRAL compendium, which provides several databases and tools to aid in the analysis of the sequences and structures of proteins classified in SCOPe. SCOPe continues high-quality manual classification of new superfamilies, a key feature of SCOP. Artifacts such as expression tags are now separated into their own class, in order to distinguish them from the homology-based annotations in the remainder of the SCOPe hierarchy. SCOPe 2.06 contains 77,439 Protein Data Bank entries, double the 38,221 structures classified in SCOP.

Keywords: database; protein evolution; structure classification.

Fig. 1. Changes to SCOP(e) design and size

All stable SCOP and SCOPe releases since the introduction of stable identifiers (SCOP 1.55, July 2001) are shown. The height of the vertical line for each release represents the number of PDB entries classified. The angle of the blue baseline between releases reflects the degree of divergence from comprehensive and fully manually curated releases. SCOP2 [31] is a major redesign of SCOP that enables curators to annotate a richer set of evolutionary relationships between proteins, providing a more precise and accurate characterization of protein relationships. SCOP2 is currently available as a prototype that classifies 995 proteins. A dashed line indicates that the SCOP2 prototype is partially based on SCOP 1.75.

Fig. 2. Examples of manual curation in SCOPe

A) Top and side views of F₁ and V₁ ATP synthase subunits; the “top” view is oriented towards the membrane. Conserved N-terminal, middle, and C-terminal subunits of the alpha and beta subunits of F₁ (A and B subunits of V₁) are shown in blue, orange, and green, respectively. The “bulge” domain of V₁, which represents a new SCOPe superfamily in 2.06, is shown in red. Other subunits of F₁ and V₁ are shown in light grey. B) Four homologous domains from bacterial toxins are colored in a spectrum ranging from blue at the N-terminal end to red at the C-terminal end. Other domains from the structures are shown in grey. C) Two homologous domains from the PA14 superfamily are colored in a spectrum ranging from blue at the N-terminal end to red at the C-terminal end. Other domains from the structures are shown in grey. PA14 was part of the Anthrax Protective Antigen fold (the entire structure shown on the left) in versions of SCOP and SCOPe prior to SCOPe 2.04.