title: 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.
authors.affiliation: Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: scope@compbio.berkeley.edu.
authors.forename: John-Marc
authors.initials: JM
authors.lastname: Chandonia
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Naomi K
authors.initials: NK
authors.lastname: Fox
authors.affiliation: Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Brenner
mesh_terms: D016477:Artifacts; D003001:Cloning, Molecular; D019295:Computational Biology; D030562:Databases, Protein; D009154:Mutation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000145:classification*
chemical_list: D011506:Proteins
keywords: database; protein evolution; structure classification