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Protocols

COPS specifications

Information


Unique identifier OMICS_34431
Name COPS
Alternative name Classification Of Protein Structure
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline COPS team

Publication for Classification Of Protein Structure

COPS citations

 (6)
library_books

Computing the origin and evolution of the ribosome from its structure — Uncovering processes of macromolecular accretion benefiting synthetic biology

2015
Comput Struct Biotechnol J
PMCID: 4823900
PMID: 27096056
DOI: 10.1016/j.csbj.2015.07.003

[…] umbers are small relative to other classification schemes, which atomize molecular structure to levels closer to the sequence level (e.g. the Pfam database ).Despite decades of effort, the systematic classification of protein structure remains limited by the lack of a general metric for global pairwise (or multiple) comparisons that can unify the widely different structural fold topologies . This […]

library_books

Computer Based Annotation of Putative AraC/XylS Family Transcription Factors of Known Structure but Unknown Function

2012
PMCID: 3312330
PMID: 22505803
DOI: 10.1155/2012/103132

[…] Scanning of the complete PDB for target proteins sharing a similar tertiary structure with a given query protein was performed with the web server COPS–TopSearch of the Center of Applied Molecular Engineering (University of Salzburg) available at http://www.came.sbg.ac.at/ []. TopSearch is a fast three-dimensional (3D) search method that relies […]

call_split

Evolutionary Innovations and the Organization of Protein Functions in Genotype Space

2010
PLoS One
PMCID: 2994758
PMID: 21152394
DOI: 10.1371/journal.pone.0014172
call_split See protocol

[…] mputed features were available. To facilitate protein comparison, we restricted our study to single domain proteins longer than 50 amino acids. The structural information we used is based on the CATH classification of protein structure domains (v.3.2.0) . Throughout, we use the concepts of structure and domain interchangeably and define it at the level of homologous superfamily.We mapped domains t […]

library_books

Fast and accurate protein substructure searching with simulated annealing and GPUs

2010
BMC Bioinformatics
PMCID: 2944279
PMID: 20813068
DOI: 10.1186/1471-2105-11-446

[…] identifiers in this table have since been obsoleted, and we replace these with their new versions according to the RCSB PDB website [,]. We perform an all-against-all comparison in this data set.The COPS Benchmark 2009/6 data set [] consists of a database of 1056 structures and a query set of 176 structures. The queries are not present in the database, and each query has exactly six true positive […]

library_books

GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains

2009
Nucleic Acids Res
PMCID: 2817468
PMID: 19923231
DOI: 10.1093/nar/gkp1049

[…] ble are not very specific. Furthermore, estimates of the error rate for the annotation of complete genomes vary from <5 to >40% depending on the types of function (,).Gene3D (), derived from the CATH classification of protein structure (), and Superfamily (), derived from the SCOP classification of protein structure (), contain predicted protein domain sequences assigned to structural domain super […]

call_split

Random Amino Acid Mutations and Protein Misfolding Lead to Shannon Limit in Sequence Structure Communication

2008
PLoS One
PMCID: 2518838
PMID: 18769673
DOI: 10.1371/journal.pone.0003110
call_split See protocol

[…] .54≈HA* bits of information are necessary to determine the structural class and architecture, i.e. the first two levels in the CATH hierarchy (the “Class Architecture Topology Homologous superfamily” classification of protein structure domains, version 2.6.0, ). HCA is the information entropy from the distribution of known structural domains among all 39 protein architectures of CATH version 2.6.0 […]

Citations

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COPS institution(s)
Center of Applied Molecular Engineering, Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Salzburg, Austria

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