CDD: a Conserved Domain Database for protein classification

@article{MarchlerBauer2005CDDAC,
  title={CDD: a Conserved Domain Database for protein classification},
  author={Aron Marchler-Bauer and John B. Anderson and Praveen F. Cherukuri and Carol DeWeese-Scott and Lewis Y. Geer and Marc Gwadz and Siqian He and David I. Hurwitz and John D. Jackson and Zhaoxi Ke and Christopher J. Lanczycki and Cynthia A. Liebert and Chunlei Liu and Fu Lu and Gabriele H. Marchler and Mikhail Mullokandov and Benjamin A. Shoemaker and Vahan Simonyan and James S. Song and Paul A. Thiessen and Roxanne A. Yamashita and Jodie J. Yin and Dachuan Zhang and Stephen H. Bryant},
  journal={Nucleic Acids Research},
  year={2005},
  volume={33},
  pages={D192 - D196}
}
The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez… 

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References

SHOWING 1-10 OF 11 REFERENCES
CDD: a database of conserved domain alignments with links to domain three-dimensional structure
The Conserved Domain Database (CDD) is a compilation of multiple sequence alignments representing protein domains conserved in molecular evolution. It has been populated with alignment data from the
CD-Search: protein domain annotations on the fly
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
CDART: protein homology by domain architecture.
The Conserved Domain Architecture Retrieval Tool (CDART) performs similarity searches of the NCBI Entrez Protein Database based on domain architecture, defined as the sequential order of conserved
SMART 4.0: towards genomic data integration
TLDR
Improvements in SMART are centred on the integration of data from completed metazoan genomes, and the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries.
Comparison of sequence and structure alignments for protein domains
TLDR
It is found that domain alignments in publicly available collections based on sequence and structure comparison are largely consistent, however, the homologous regions identified by sequence comparison are often shorter than those identified by 3D structure comparison.
The COG database: an updated version includes eukaryotes
TLDR
A major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes is described and is expected to be a useful platform for functional annotation of newlysequenced genomes, including those of complex eukARYotes, and genome-wide evolutionary studies.
The last CTD repeat of the mammalian RNA polymerase II large subunit is important for its stability.
TLDR
It is shown that removal or severe disruption of the last CTD repeat, but not point mutation of its CKII sites, results in its proteolytic degradation to the Pol IIb form in vivo, but does not appear to affect the specific transcription of genes.
Cn3D: sequence and structure views for Entrez.
andNatale,D.A. (2003)TheCOGdatabase:andupdated version includes eukaryotes
  • BMC Bioinformatics,
  • 2003
0: towards genomic data integration
  • Nucleic Acids Res
  • 2004
...
...