Conserved Domain Database: Difference between revisions

Revision as of 03:36, 5 December 2011

Latest revision as of 03:12, 21 April 2025

(29 intermediate revisions by 22 users not shown)

Line 1:

{{Short description|Biological database}}

{{infobox biodatabase

|title = CDD

Line 8 ⟶ 9:

|laboratory =

|author = Aron Marchler-Bauer

|pmidcitation = Marchler-Bauer & al. (20112013)<ref name="pmid21109532CDD reference"/>

|released = 2003

|standard =

|format =

|url = httphttps://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

|download =

|webservice =

Line 27 ⟶ 28:

}}

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="pmid21109532CDD reference">{{citeCite journal | author = Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH | title = CDD: a Conserved Domain Database for the functional annotation of proteins | journal = Nucleic Acids Res. | volume = 39 | issue = Database issue | pages = D225–9 | year = 2011 | month = January | pmid = 21109532 | pmc = 3013737 | doi = 10.1093/nar/gkq1189 }}</ref>

| 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> The database consists of position-specific score matrices and serves as resource for protein annotation such as identification of conserved ___domain or inference of functional site.<ref>{{Cite journal |last=Marchler-Bauer |first=Aron |last2=Lu |first2=Shennan |last3=Anderson |first3=John B. |last4=Chitsaz |first4=Farideh |last5=Derbyshire |first5=Myra K. |last6=DeWeese-Scott |first6=Carol |last7=Fong |first7=Jessica H. |last8=Geer |first8=Lewis Y. |last9=Geer |first9=Renata C. |last10=Gonzales |first10=Noreen R. |last11=Gwadz |first11=Marc |last12=Hurwitz |first12=David I. |last13=Jackson |first13=John D. |last14=Ke |first14=Zhaoxi |last15=Lanczycki |first15=Christopher J. |date=2011-01-01 |title=CDD: a Conserved Domain Database for the functional annotation of proteins |url=https://academic.oup.com/nar/article/39/suppl_1/D225/2507607 |journal=Nucleic Acids Research |volume=39 |issue=suppl_1 |pages=D225–D229 |doi=10.1093/nar/gkq1189 |issn=0305-1048|pmc=3013737 }}</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.

The goal of the NCBI conserved ___domain curation project is to provide database users with insights into how patterns of residue conservation and divergence in a family relate to functional properties, and to provide useful links to more detailed information that may help to understand those sequence/structure/function relationships. To do this, CDD Curators include the following types of information in order to supplement and enrich the traditional multiple sequence alignments that form the foundation of ___domain models: 3-dimensional structures and conserved core motifs, conserved features/sites, phylogenetic organization, links to electronic literature resources.

==Content==

CDD content includes NCBI manually curated ___domain models and ___domain models imported from a number of external source databases ([[Pfam]], SMART, COG, PRK, TIGRFAM[[TIGRFAMs]]). What is unique about NCBI-curated domains is that they use 3D-structure information to explicitly define ___domain boundaries, align blocks, amend alignment details, and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe ___domain families that are clearly related by common descent. To provide a non-redundant view of the data, CDD clusters similar ___domain models from various sources into superfamilies.

==Searching the database==

The collection is also part of NCBI’sNCBI's [[Entrez]] query and retrieval system, crosslinked to numerous other resources. CDD provides annotation of ___domain footprints and conserved functional sites on protein sequences. Precalculated ___domain annotation can be retrieved for protein sequences tracked in NCBI’sNCBI's Entrez system, and CDD’sCDD's collection of models can be queried with novel protein sequences via * {{cite web | url = httphttps://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi| title = the CD-Search service | author = | authorlink = | coauthors = | date = | format = | work = | publisher = United States National Center for Biotechnology Information | pages = | language = | archiveurl = | archivedate = | quote = | accessdate = }}, or at* {{cite web | url = httphttps://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi| title = the Batch CD-Search | author = | authorlink = | coauthors = | date = | format = | work = | publisher = United States National Center for Biotechnology Information | pages = | language = | archiveurl = | archivedate = | quote = | accessdate = }}, that allows the computation and download of annotation for large sets of protein queries.

==References==

Line 45 ⟶ 73:

==External links==

* {{cite web | url = httphttps://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml | title = Conserved Domains Database (CDD) and Resource Group | author = | authorlink = | coauthors = | date = | format = | work = | publisher = United States National Center for Biotechnology Information | pages = | language = | archiveurl = | archivedate = | quote = | accessdate = }}

{{Biodatabase-stub}}

[[Category:BiologicalProtein databases]]

[[Category:Protein structure]]

[[Category:Protein domains]]