CDD: a curated Entrez database of conserved domain alignments

By Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, N. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, A. Jacobs, Christopher J. Lanczycki and 17 more. Nucleic Acids Res., 2003

788 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/a5375b684c8e6640246df2eaec5f59b2ef94242b

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Citations in the corpus

Enzyme-specific profiles for genome annotation: PRIAM. (2003, methodology): “The ﬁrst step is a homology search between each protein and PRIAM proﬁles using the RPS-BLAST program (18), ﬁltered for E-values below 10 –10 .”
SCOPmap: Automated assignment of protein structures to evolutionary superfamilies (2004, methodology): “The gapped BLAST [41], RPS-BLAST[42], PSI-BLAST [41], COMPASS [43], MAMMOTH [19], and DaliLite [44] tools are used in SCOPmap.”
CD-Search: protein domain annotations on the fly (2004, background): “Curators at the NCBI are adding in an ongoing manner models for ancient, phylogenetically widespread domain families with structure-based alignments and explicitly recorded subfamily hierarchies (4).”
Nature of the protein universe (2009, methodology): “For a sequence to be modelable in this way, it must align well to a known structure, and this is likely to be achieved because RPS-BLAST is a fairly conservative alignment method (31).”
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes (2004, methodology): “Briefly, the KOG construction protocol included: First, the detection and masking of common, repetitive domains using the RPSBLAST program and the PSSMs for the respective domains from the CDD collection [81]; second, all-against-all comparison of protein sequences from the analyzed genomes using th”
A novel method for accurate operon predictions in all sequenced prokaryotes (2005, methodology): “To determine COG function codes, we assigned genes to COGs (13) via reverse position-specific BLAST (18) against CDD (19), or by using COG membership from NCBI.”
The Biomolecular Interaction Network Database and related tools 2005 update (2004, background): “SMID-BLAST matches a protein sequence query to a CDD domain (18), thereby returning the set of Figure 1.”
CDD: NCBI's conserved domain database (2014, methodology): “12, contains 46 675 protein- and protein domain-models, with content obtained from Pfam (1), SMART (2), the COGs collection (3), TIGRFAMs (4), the NCBI Protein Clusters collection (5) and NCBI’s in-house data curation effort (6).”
CDD: specific functional annotation with the Conserved Domain Database (2008, neutral): “A new version of CDTree/Cn3D has been made available recently, which now supports Mac OSX as well as Windows operating systems and extends the number of features.”
Database resources of the National Center for Biotechnology Information: update (2004, methodology): “Alignment-based protein domain information from the CDD and 3D domains from the MMDB are searchable via the Entrez interface.”
The COG database: an updated version includes eukaryotes (2003, methodology): “Detection and masking of widespread, typically repetitive domains, which was performed by using the RPSBLAST program and the PSSMs for the respective domains from the CDD collection [40].”