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CDD Help

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Help on CD-Search and Databases

CD-Search

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CDART

Conserved Domain Architecture Retrieval Tool

Smart

Pfam: US / UK

COG

Explore CDD's source databases


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NCBI's structure database

Cn3D v4.1

3D-structure viewer

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Structure comparisons

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Research topics and staff


A Conserved Domain Database and Search Service, v2.02

Proteins often contain several modules or domains, each with a distinct evolutionary origin and function. The CD-Search service may be used to identify the conserved domains present in a protein sequence:

Run CD-Search:

Search Database:
Enter Protein query as Accession, Gi, or Sequence in FASTA format:
Read about FASTA format description, click here for advanced options.


Computational biologists define conserved domains based on recurring sequence patterns or motifs. CDD currently contains domains derived from two popular collections, Smart and Pfam, plus contributions from colleagues at NCBI, such as COG. The source databases also provide descriptions and links to citations. Since conserved domains correspond to compact structural units, CDs contain links to 3D-structure via Cn3D whenever possible.




in Entrez:

(short names, accessions, and descriptions have been indexed)

To identify conserved domains in a protein sequence, the CD-Search service employs the reverse position-specific BLAST algorithm. The query sequence is compared to a position-specific score matrix prepared from the underlying conserved domain alignment. Hits may be displayed as a pairwise alignment of the query sequence with a representative domain sequence, or as a multiple alignment. CD-Search now is run by default in parallel with protein BLAST searches. While the user waits for the BLAST queue to further process the request, the domain architecture of the query may already be studied.

Run CDART, the Conserved Domain Architecture Retrieval Tool to search for proteins with similar domain architectures. CDART uses precomputed CD-search results to quickly identify proteins with a set of domains similar to that of the query.

Read more about CDD:

Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Research 32:W327-331 (2004) . [Abstract] [Full Text]

Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Research 31:383-387 (2003) . [Abstract] [Full Text][Terms]

Marchler-Bauer, A., Panchenko, A.R.,Shoemaker, B.A., Thiessen, P.A., Geer, L.Y. and Bryant, S.H. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Research 30:281-283 (2002) . [Abstract] [Full Text]



Updated 10/28/04

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