Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2004 Jul 1;32(Web Server issue):W327-31.
doi: 10.1093/nar/gkh454.

CD-Search: protein domain annotations on the fly

Aron Marchler-Bauer  1 , Stephen H Bryant
Affiliations

CD-Search: protein domain annotations on the fly

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

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.

PubMed Disclaimer

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.
See this image and copyright information in PMC

Similar articles

  • CDD: a database of conserved domain alignments with links to domain three-dimensional structure.
    Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH. Marchler-Bauer A, et al. Nucleic Acids Res. 2002 Jan 1;30(1):281-3. doi: 10.1093/nar/30.1.281. Nucleic Acids Res. 2002. PMID: 11752315 Free PMC article.
  • CDD: a Conserved Domain Database for protein classification.
    Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, 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. Marchler-Bauer A, et al. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D192-6. doi: 10.1093/nar/gki069. Nucleic Acids Res. 2005. PMID: 15608175 Free PMC article.
  • CDD: a conserved domain database for interactive domain family analysis.
    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 CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH. Marchler-Bauer A, et al. Nucleic Acids Res. 2007 Jan;35(Database issue):D237-40. doi: 10.1093/nar/gkl951. Epub 2006 Nov 29. Nucleic Acids Res. 2007. PMID: 17135202 Free PMC article.
  • CDD: a curated Entrez database of conserved domain alignments.
    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. Marchler-Bauer A, et al. Nucleic Acids Res. 2003 Jan 1;31(1):383-7. doi: 10.1093/nar/gkg087. Nucleic Acids Res. 2003. PMID: 12520028 Free PMC article.
  • CDD: specific functional annotation with the Conserved Domain Database.
    Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH. Marchler-Bauer A, et al. Nucleic Acids Res. 2009 Jan;37(Database issue):D205-10. doi: 10.1093/nar/gkn845. Epub 2008 Nov 4. Nucleic Acids Res. 2009. PMID: 18984618 Free PMC article.
See all similar articles

Cited by

See all "Cited by" articles

References

    1. Bateman A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M., Moxon,S., Sonnhammer,E.L., Studholme,D.J., Yates,C. and Eddy,S.R. (2004) The Pfam protein families database. Nucleic Acids Res., 32, 138–141. - PMC - PubMed
    1. Letunic I., Copley,R.R., Schmidt,S., Ciccarelli,F.D., Doerks,T., Shultz,J., Ponting,C.P. and Bork,P. (2004) SMART 4.0: towards genomic data integration. Nucleic Acids Res., 32, 142–144. - PMC - PubMed
    1. Tatusov R.L, Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V, Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N., Rao,B.S., Smirnov,S., Sverdlov,A.V., Vasudevan,S., Wolf,Y.I., Yin,J.J. and Natale,D.A. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41. - PMC - PubMed
    1. Marchler-Bauer A., Anderson,J.B., DeWeese-Scott,C., Fedorova,N.D., Geer,L.Y., He,S., Hurwitz,D.I., Jackson,J.D., Jacobs,A.R., Lanczycki,C.J., Liebert,C.A., Liu,C., Madej,T., Marchler,G.H., Mazumder,R., Nikolskaya,A.N., Panchenko,A.R., Rao,B.S., Shoemaker,B.A., Simonyan,V., Song,J.S., Thiessen,P.A., Vasudevan,S., Wang,Y., Yamashita,R.A., Yin,J.J. and Bryant,S.H. (2003) CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res., 31, 383–387. - PMC - PubMed
    1. Altschul S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. - PMC - PubMed
  NODES
INTERN 1
twitter 2