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CDD: NCBI's conserved domain database.

Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH - Nucleic Acids Res. (2014)

Bottom Line: We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort.The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available.CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA bauer@ncbi.nlm.nih.gov.

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CD-Search reporting a ‘rescued’ domain annotation, which scores an E-value above the default reporting threshold of 0.01. The live search for the query sequence, derived from the PDB structure 2WOZ.
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Figure 1: CD-Search reporting a ‘rescued’ domain annotation, which scores an E-value above the default reporting threshold of 0.01. The live search for the query sequence, derived from the PDB structure 2WOZ.

Mentions: If additional domain hits that score above the default reporting E-value threshold are tandem repeats of a neighboring domain that was detected at the default E-value threshold, they are reported irrespective of the domain architecture's frequency in the NR database. Figure 1 shows the result of such a live search, for a query sequence derived from the PDB structure 2WOZ (11), as tracked by MMDB (12). In this example, an additional hit to a domain model is reported which is already found several times in a tandem repeat arrangement.


CDD: NCBI's conserved domain database.

Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH - Nucleic Acids Res. (2014)

CD-Search reporting a ‘rescued’ domain annotation, which scores an E-value above the default reporting threshold of 0.01. The live search for the query sequence, derived from the PDB structure 2WOZ.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4383992&req=5

Figure 1: CD-Search reporting a ‘rescued’ domain annotation, which scores an E-value above the default reporting threshold of 0.01. The live search for the query sequence, derived from the PDB structure 2WOZ.
Mentions: If additional domain hits that score above the default reporting E-value threshold are tandem repeats of a neighboring domain that was detected at the default E-value threshold, they are reported irrespective of the domain architecture's frequency in the NR database. Figure 1 shows the result of such a live search, for a query sequence derived from the PDB structure 2WOZ (11), as tracked by MMDB (12). In this example, an additional hit to a domain model is reported which is already found several times in a tandem repeat arrangement.

Bottom Line: We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort.The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available.CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg. 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA bauer@ncbi.nlm.nih.gov.

Show MeSH