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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 results for SwissProt Q6XUD6, zoomed in to ‘residue level’ display so that the precise locations of domain boundaries and functional sites become apparent. Query sequence residues highlighted in bold print have been identified as part of a functional site (such as the ‘catalytic site’ mapping to R118 and D151, plus other residues not shown in this example). Structural motifs are shown as double-headed arrows.
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Figure 2: CD-Search results for SwissProt Q6XUD6, zoomed in to ‘residue level’ display so that the precise locations of domain boundaries and functional sites become apparent. Query sequence residues highlighted in bold print have been identified as part of a functional site (such as the ‘catalytic site’ mapping to R118 and D151, plus other residues not shown in this example). Structural motifs are shown as double-headed arrows.

Mentions: CDD curators record the location of functional motifs on protein domain models, so that these motifs can be mapped onto protein sequences and facilitate the interpretation of sequence conservation and variation, for example. Site annotations provided by CDD include a large number of active sites, chemical binding and protein-protein interaction sites, and complement, to some extent, experimentally derived or computationally generated site annotations tied to individual protein records, such as found in the SwissProt data set (13), for example. We have now added ‘structural motifs’ to the list of motifs or sites that may be recorded and mapped. Structural motifs are not necessary functional, but provide more detailed annotation on query sequences. They will include short structural repeats, such as beta-propellers, coiled coils and transmembrane segments, as well as short functional motifs, such as DNA-binding zinc fingers, for example. Upcoming versions of CDD will contain a novel type of model, called a ‘structural domain’, with the accession prefix ‘sd’. Structural domain models are being assembled solely for the purpose of providing structural motif annotation, but structural motif annotation can also be found on regular conserved domain models with the accession prefix ‘cd’. Figure 2 gives an example of how such structural motif annotation delineates the extent of beta-propellers on a query sequence from an Influenza virus. Figure 2 also displays a novel feature of the CD-Search interface, the ability to zoom the graphical displays so that individual query sequence residues become visible and let the user map domain extents and the location of conserved sites more precisely. Individual residues that are parts of functional sites (but not structural motifs) are highlighted in bold font.


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 results for SwissProt Q6XUD6, zoomed in to ‘residue level’ display so that the precise locations of domain boundaries and functional sites become apparent. Query sequence residues highlighted in bold print have been identified as part of a functional site (such as the ‘catalytic site’ mapping to R118 and D151, plus other residues not shown in this example). Structural motifs are shown as double-headed arrows.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: CD-Search results for SwissProt Q6XUD6, zoomed in to ‘residue level’ display so that the precise locations of domain boundaries and functional sites become apparent. Query sequence residues highlighted in bold print have been identified as part of a functional site (such as the ‘catalytic site’ mapping to R118 and D151, plus other residues not shown in this example). Structural motifs are shown as double-headed arrows.
Mentions: CDD curators record the location of functional motifs on protein domain models, so that these motifs can be mapped onto protein sequences and facilitate the interpretation of sequence conservation and variation, for example. Site annotations provided by CDD include a large number of active sites, chemical binding and protein-protein interaction sites, and complement, to some extent, experimentally derived or computationally generated site annotations tied to individual protein records, such as found in the SwissProt data set (13), for example. We have now added ‘structural motifs’ to the list of motifs or sites that may be recorded and mapped. Structural motifs are not necessary functional, but provide more detailed annotation on query sequences. They will include short structural repeats, such as beta-propellers, coiled coils and transmembrane segments, as well as short functional motifs, such as DNA-binding zinc fingers, for example. Upcoming versions of CDD will contain a novel type of model, called a ‘structural domain’, with the accession prefix ‘sd’. Structural domain models are being assembled solely for the purpose of providing structural motif annotation, but structural motif annotation can also be found on regular conserved domain models with the accession prefix ‘cd’. Figure 2 gives an example of how such structural motif annotation delineates the extent of beta-propellers on a query sequence from an Influenza virus. Figure 2 also displays a novel feature of the CD-Search interface, the ability to zoom the graphical displays so that individual query sequence residues become visible and let the user map domain extents and the location of conserved sites more precisely. Individual residues that are parts of functional sites (but not structural motifs) are highlighted in bold font.

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