A Conserved Domain Database and Search Service, v2.15

Proteins often contain several modules or domains, each with a distinct evolutionary origin and function. NCBI's Conserved Domain Database is a collection of multiple sequence alignments for ancient domains and full-length proteins. The CD-Search service may be used to identify the conserved domains present in a protein query sequence:

Computational biologists define conserved domains based on recurring sequence patterns or motifs. The un-curated section of CDD contains domains imported from SMART, Pfam and COGs. The source databases also provide descriptions and links to citations. Because conserved domains correspond to compact structural units, CDs are linked to 3D structure when possible. The NCBI-curated section of CDD attempts to group ancient domains related by common descent into family hierarchies.

To identify conserved domains in a protein sequence, the CD-Search service uses 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 alignments of the query sequence with representative domain sequences, or as multiple alignments. CD-Search now is run by default in parallel with protein BLAST searches. Although 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 pre-computed 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, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki C, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 2007;35(Database Issue):D237-40. [Full Text]

Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki C, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 2005;33 Database Issue:D192-6. [Abstract] [Full Text]

Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004;32(Web Server issue):W327-31. [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 Res. 2003;31:383-7. [Abstract] [Full Text][Terms]

Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, and Bryant SH CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 2002;30:281-3. [Abstract] [Full Text]