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ECOD specifications

Information


Unique identifier OMICS_14027
Name ECOD
Alternative name Evolutionary Classification Of protein Domains
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainers


  • person_outline Nick Grishin
  • person_outline Richard Dustin Schaeffer

Publications for Evolutionary Classification Of protein Domains

ECOD citations

 (11)
library_books

Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

2017
Proc Natl Acad Sci U S A
PMCID: 5676897
PMID: 29078314
DOI: 10.1073/pnas.1707642114

[…] hm to optimally identify themes of different lengths and use it to analyze reuse in two datasets of proteins of known structure: (i) a set of 28,223 [70% nonredundant (NR)] domains referred to as the ECOD dataset and (ii) a set of 31,417 (70% NR; Sep6_2014) chains referred to as the Protein Data Bank (PDB) dataset. Using HHSearch (), we align all-vs.-all within these sets and calculate for each si […]

library_books

Detecting similar binding pockets to enable systems polypharmacology

2017
PLoS Comput Biol
PMCID: 5490940
PMID: 28662117
DOI: 10.1371/journal.pcbi.1005522

[…] To calculate sequence similarity of proteins, we applied JackHMMER with default parameters [], E-value < 10−4. As for the fold annotation of structures, we used the classification of ECOD (January 2015) at level 4 of the hierarchy []. […]

library_books

An ambiguity principle for assigning protein structural domains

2017
Sci Adv
PMCID: 5235333
PMID: 28097215
DOI: 10.1126/sciadv.1600552

[…] n structures. We have shown that our A-index is sensitive to ambiguous cases of structural domain assignment. Some structures show a high A-index despite having the same annotation in CATH, SCOP, and ECOD. These cases may fall into the category of proteins that have alternative, yet undiscovered, biological functions. Thus, future work will investigate how measuring the architectural complexity of […]

library_books

A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

2017
eLife
PMCID: 5468089
PMID: 28527238
DOI: 10.7554/eLife.26111.048

[…] family of proteases that form the catalytic core of the proteasome (; ; ; ). These proteases are the most structurally similar family to PP2C phosphatases as revealed using the DALI server () and the ECOD database (), and like PP2C phosphatases their catalytic activity is subject to allosteric regulation. Specifically, the proteasome proteases and PP2C phosphatases have a conserved core fold (), w […]

library_books

Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

2016
PLoS Comput Biol
PMCID: 4822843
PMID: 27049771
DOI: 10.1371/journal.pcbi.1004862

[…] ily are more related to each other, thus fully justifying a separate superfamily designation. Satisfactorily, homologous relationships between Cache, PAS, and GAF were also captured in a new database ECOD (Evolutionary Classification of Protein Domains) [], which also included most of the related “orphan” families described above into the same superfamily.A key unsolved biological problem in signa […]

library_books

An Ancient Fingerprint Indicates the Common Ancestry of Rossmann Fold Enzymes Utilizing Different Ribose Based Cofactors

2016
PLoS Biol
PMCID: 4777477
PMID: 26938925
DOI: 10.1371/journal.pbio.1002396

[…] chitecture Topology Homologous superfamilies), define these classes as separate superfamilies []. However, based amongst other considerations on the shared β2-Asp/Glu motif, other classifiers such as ECOD (Evolutionary Classification of Protein Domains) [] or Interpro [] classify all three classes (NAD(P), FAD, and SAM-dependent Rossmann enzymes) in the same homology group [,,,,].Overall, a common […]

Citations

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ECOD institution(s)
Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
ECOD funding source(s)
Supported in part by the National Institutes of Health (GM094575) and the Welch Foundation (I-1505).

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