CDD: conserved domains and protein three-dimensional structure

By Aron Marchler-Bauer, Chanjuan Zheng, Farideh Chitsaz, Myra K. Derbyshire, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki and 8 more. Nucleic Acids Res., 2012

883 citations recorded by the source corpus.

CDD, the Conserved Domain Database, is part of NCBI’s Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. Pre-computed annotation is available via Entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences, utilizing RPS-BLAST to rapidly identify putative matches. CDD incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and well-characterized protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature. To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/5dc7237f225f72fcbca8cef7bcb83591a14608a1

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Citations in the corpus

Expanded microbial genome coverage and improved protein family annotation in the COG database (2014, methodology): “Certain COG names have been updated by the authors of this work on an ad hoc basis and these corrections have been included in the CDD (3).”
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides (2015, methodology): “If no hits can be retrieved with the afore-mentioned procedure, we scan the CDD database (42) using the ‘hmmscan’ program from the HMMER3 suite (43).”
The Phyre2 web portal for protein modelling, prediction and analysis (2015, neutral): “See Steps 25–28 of the PROCEDURE for details on alignment interpretation.”
Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes (2015, methodology): “For every proteinencoding gene in the PubSEED platform, it is possible to examine the NCBI Conserved Domains Database (CDD) (Marchler-Bauer et al., 2013).”
MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. (2019, methodology): “Mercator relied on sequence similarity and, when appropriate, protein domains from InterPro (Mulder and Apweiler, 2007) and CDD (Marchler-Bauer et al., 2013) that had been manually assigned to the bins.”
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) (2013, methodology): “For each protein in a genome, the SEED Web site offers a protein page that contains direct links to the NCBI CDD database (16), the KEGG Enzyme database (15) and PubMed ID links to articles describing the functional role of a given gene product (11) (15 565 links).”
GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis (2013, neutral): “Database (30) and Protein Clusters Database (31), in addition to the COG”