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CD-Search: protein domain annotations on the fly - PubMed

  • ️Thu Jan 01 2004

. 2004 Jul 1;32(Web Server issue):W327-31.

doi: 10.1093/nar/gkh454.

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CD-Search: protein domain annotations on the fly

Aron Marchler-Bauer et al. Nucleic Acids Res. 2004.

Abstract

We describe the Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences. CD-Search uses BLAST(R) heuristics to provide a fast, interactive service, and searches a comprehensive collection of domain models. Search results are displayed as domain architecture cartoons and pairwise alignments between the query and domain-model consensus sequences. Search results may be visualized in further detail by embedding the query sequence into multiple alignment displays and by mapping onto three-dimensional molecular graphic displays of known structures within the domain family. CD-Search can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi.

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Figures

Figure 1
Figure 1

Graphical summary of results and hit list. The query sequence used in this search was gi|116863 (9).

Figure 2
Figure 2

A fragment of the query sequence embedded in the domain alignment for hemopexin-like repeats. Conserved features (metal binding sites) are indicated with hash marks on top of aligned columns.

Figure 3
Figure 3

Alignment visualization in the context of 3D structure. The query sequence has been added to the domain-alignment model. In this particular view the user visualizes evidence for the metal binding site (a conserved feature of this family), which is provided by the solved 3D structure of a protein–metal complex.

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