SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures
Open accessAbstract
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.
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- Authors
- Fox, N. K., Brenner, S. E., & Chandonia, J.-M.
- Affiliations
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Brenner, Steven E.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-12-03
- Volume
- 42
- Issue
- D1
- Pages
- D304-D309
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3965108
- OpenAlex
- W2161072217
- Cited by
- 762
- References
- 12
- Citations by year
- 2026: 37 · 2025: 42 · 2024: 49 · 2023: 49 · 2022: 86 · 2021: 87 · 2020: 88 · 2019: 72 · 2018: 56 · 2017: 60 · 2016: 65 · 2015: 51 · 2014: 18 · 2013: 1
- FWCI
- 20.44
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- U.S. Department of Energy (-AC02-05CH11231, Contract No. DE-AC02-05-CH11231, 05CH11231, No. DE-AC02-05-CH11231, DE AC02 05CH11231, DE-AC02-)
- National Institutes of Health (5r01gm073109-08, DE-AC02–05CH11231, R01-GM073109)
- National Institute of General Medical Sciences (R01-GM073109)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- scope, SCOP, ASTRAL, protein structure classification, protein structure database, algorithmic curation, benchmarking, Protein Data Bank, protein evolution, structural relationships
- MeSH terms
- Proteins, Protein Structure, Tertiary, Systems Integration, Internet, Databases, Protein
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