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The '''Conserved Domain Database''' ('''CDD''') is a database of well-annotated [[multiple sequence alignment]] models and derived database search models, for ancient [[Protein ___domain|domains]] and full-length proteins.<ref name="CDD reference">{{
| last1 = Marchler-Bauer | first1 = A.
| last2 = Zheng | first2 = C.
| last3 = Chitsaz | first3 = F.
| last4 = Derbyshire | first4 = M. K.
| last5 = Geer | first5 = L. Y.
| last6 = Geer | first6 = R. C.
| last7 = Gonzales | first7 = N. R.
| last8 = Gwadz | first8 = M.
| last9 = Hurwitz | first9 = D. I.
| last10 = Lanczycki
| doi = 10.1093/nar/gks1243 | first10 = C. J.
| last11 = Lu | first11 = F.
| last12 = Lu | first12 = S.
| last13 = Marchler | first13 = G. H.
| last14 = Song | first14 = J. S.
| last15 = Thanki | first15 = N.
| last16 = Yamashita | first16 = R. A.
| last17 = Zhang | first17 = D.
| last18 = Bryant | first18 = S. H.
| title = CDD: Conserved domains and protein three-dimensional structure
| journal = Nucleic Acids Research
| volume = 41
| issue = Database issue
| pages = D348–D352
| year = 2012
| pmid = 23197659
| pmc =3531192
}}</ref>
==Philosophy==
Domains can be thought of as distinct functional and/or structural units of a protein. These two classifications coincide rather often, as a matter of fact, and what is found as an independently folding unit of a polypeptide chain also carries specific function. Domains are often identified as recurring (sequence or structure) units, which may exist in various contexts. In molecular evolution such domains may have been utilized as building blocks, and may have been recombined in different arrangements to modulate protein function. CDD defines conserved domains as recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis.
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