SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database

Chandonia, John-Marc; Fox, Naomi K.; Brenner, Steven E.

doi:10.1093/nar/gky1134

Title: SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database

Journal Article · 29 November 2018 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gky1134 · OSTI ID:1625572

^[1]; Fox, Naomi K. ^[2];

^[3]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; DOE/OSTI
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; Univ. of California, Berkeley, CA (United States). Department of Plant and Microbial Biology

The SCOPe (Structural Classification of Proteins—extended, https://scop.berkeley.edu) database hierarchically classifies domains from the majority of proteins of known structure according to their structural and evolutionary relationships. SCOPe also incorporates and updates the ASTRAL compendium, which provides multiple databases and tools to aid in the analysis of the sequences and structures of proteins classified in SCOPe. Protein structures are classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.07, we have focused our manual curation efforts on larger protein structures, including the spliceosome, proteasome and RNA polymerase I, as well as many other Pfam families that had not previously been classified. Domains from these large protein complexes are distinctive in several ways: novel non-globular folds are more common, and domains from previously observed protein families often have N- or C-terminal extensions that were disordered or not present in previous structures. The current monthly release update, SCOPe 2.07–2018-10–18, classifies 90 992 PDB entries (about two thirds of PDB entries).

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625572

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 47; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation Bertram, Karl; Agafonov, Dmitry E.; Dybkov, Olexandr Cell, Vol. 170, Issue 4 https://doi.org/10.1016/j.cell.2017.07.011	journal	August 2017
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Data growth and its impact on the SCOP database: new developments Andreeva, A.; Howorth, D.; Chandonia, J. -M. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm993	journal	December 2007
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SCOP2 prototype: a new approach to protein structure mining Andreeva, Antonina; Howorth, Dave; Chothia, Cyrus Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1242	journal	November 2013
CATH: comprehensive structural and functional annotations for genome sequences Sillitoe, Ian; Lewis, Tony E.; Cuff, Alison Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku947	journal	October 2014
The Pfam protein families database: towards a more sustainable future Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1344	journal	December 2015
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