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Protocols

SCOPe specifications

Information


Unique identifier OMICS_03034
Name SCOPe
Alternative names Structural Classification of Proteins–extended, SCOP2, SCOP
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Version 2.07
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Structural_Classification_of_Proteins_database

Maintainers


  • person_outline SCOPe Team
  • person_outline Alexey Murzin

Additional information


http://scop.mrc-lmb.cam.ac.uk/scop/

Publications for Structural Classification of Proteins–extended

SCOPe citations

 (9)
library_books

Protein sequence similarity search acceleration using a heuristic algorithm with a sensitive matrix

2017
J Struct Funct Genomics
PMCID: 5274646
PMID: 28083762
DOI: 10.1007/s10969-016-9210-4

[…] COP. Because of the database size difference, LAST performance against CATH20-SCOP saturates earlier than that against UniRef50+ approximately at m = 103. The ROC curve trends resemble the curves for SCOP20 validation (Fig. ), indicating that LAST with MIQS is as sensitive as CS-BLAST and SEARCH with BLOSUM62. Fig. 3 […]

library_books

Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling

2016
Biochem Soc Trans
PMCID: 5011417
PMID: 27284063
DOI: 10.1042/BST20160053

[…] d by different sequence comparison algorithms []. Numerous exceptions observed to topological rules, along with complex evolutionary scenarios and unusual protein features prompted the development of SCOP2, a successor of the SCOP database []. Here, I review selected cases of structural variations and peculiarities in individual proteins and among group of homologues. Knowledge of these cases may […]

library_books

Endonuclease domain of non LTR retrotransposons: loss of function mutants and modeling of the R2Bm endonuclease

2016
Nucleic Acids Res
PMCID: 4838377
PMID: 26961309
DOI: 10.1093/nar/gkw134

[…] I homing intron endonucleases and certain Holliday junction resolvases (,). Members of the PD-(D/E)XK superfamily adopt a common structural core—a restriction endonuclease-like fold (terminology from SCOP2 database)—consisting of a four-stranded, mixed β-sheet flanked by two α-helices on both sides (αβββαβ topology) (–). Endonucleases of this family perform various biological roles, including thei […]

library_books

The history of the CATH structural classification of protein domains

2015
Biochimie
PMCID: 4678953
PMID: 26253692
DOI: 10.1016/j.biochi.2015.08.004

[…] y result in relatives possessing somewhat different folds . CATH has dealt with this by providing information on structural relatives for each domain, whilst SCOP has recently launched a new resource SCOP2 that captures these interesting relationships in more detail . […]

library_books

The value of protein structure classification information—Surveying the scientific literature

2015
Proteins
PMCID: 4609302
PMID: 26313554
DOI: 10.1002/prot.24915

[…] in the SCOP hierarchy is 68% in SCOPe 2.05, compared with 38% of current protein structures that were classified in SCOP 1.75 (which classified 67% of structures available at the time). By contrast, SCOP2 is currently a prototype. This resource is a major redesign of SCOP that enables curators to annotate a richer set of evolutionary relationships between proteins, providing a more precise and ac […]

call_split

Structure and function of the N‐terminal domain of the human mitochondrial calcium uniporter

2015
EMBO Rep
PMCID: 4662854
PMID: 26341627
DOI: 10.15252/embr.201540436
call_split See protocol

[…] Superposition of structures was performed using the CCP4 program LSQKAB , PyMOL align and Coot SSM superpose . LSQKAB was also used to estimate RMSD (Å) scores for the Cα atoms . The SCOP2 , Dali program and CATH database searches were performed using MCU NTD as a template. The Ramachandran statistics were calculated using the program MolProbity . The sequence conservation of MC […]

Citations

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SCOPe institution(s)
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
SCOPe funding source(s)
Supported by the National Institutes of Health [R01-GM073109] through the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

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