CDD: NCBI's conserved domain database

By Aron Marchler-Bauer, Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Farideh Chitsaz, Lewis Y. Geer, Renata C. Geer, Jane He, Marc Gwadz, David I. Hurwitz and 10 more. Nucleic Acids Res., 2014

3,290 citations recorded by the source corpus.

NCBI's CDD, the Conserved Domain Database, enters its 15th year as a public resource for the annotation of proteins with the location of conserved domain footprints. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

Subfields: Molecular Biology

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Citations in the corpus

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis (2016, background): “PDB70, SCOPe95 (19), Pfam (17), CDD (20), representative proteomes] and also allow users to upload their own sequence databases.”
Metabolic network analysis reveals microbial community interactions in anammox granules (2017, positive): “Manual searches were also performed across all genomes based on gene annotations, and protein domains with hydrolytic activity were subsequently conﬁrmed based on queries against the NCBI’s Conserved Domain Database 67 and Pfam database 68 using MOTIF (http://www.genome.jp/tools/motif/).”
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. (2017, neutral): “…2016) https://figshare.com/articles/Green_algal_ transcriptomes_for_phylogenetics_and_ comparative_genomics/1604778 NCBI Conserved Domain Database (Marchler-Bauer et al., 2015) https://www.ncbi.nlm.nih.gov/Structure/cdd/ wrpsb.cgi PROSITE (Sigrist et al., 2013)…”
UCSF ChimeraX: Meeting modern challenges in visualization and analysis (2018, background): “9 While the Worldwide Protein Data Bank (wwPDB) 10 is still the leading repository for experimentally solved atomic structures, many other repositories are of interest to researchers: Mod-Base 11 for predicted atomic structures; EMDB 12 for electron microscopy maps; and sequence and domain databases”
Database resources of the National Center for Biotechnology Information (2014, methodology): “In addition, CDD includes superfamily records that contain sets of CDs from one or more source databases that generate overlapping annotation on the same protein sequences.”
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures (2016, methodology): “15, contains 48 963 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).”
UCSF ChimeraX: Structure visualization for researchers, educators, and developers (2020, background): “…solved Eric F. Pettersen and Thomas D. Goddard contributed equally to this work. atomic structures, other highly used resources include ModBase 9 for predicted atomic structures; EMDataBank 10 for electron microscopy density maps; and NCBI 11,12 and UniProt 13 for sequences, just to name a few.”
The Papillomavirus Episteme: a major update to the papillomavirus sequence database (2016, background): “COBALT leverages information present in several databases (conserved domain database (32) and”
RefSeq: an update on prokaryotic genome annotation and curation (2017, background): “A notable set of proteins annotated by CDD-SPARCLE architectures was response regulator proteins.”
InterPro in 2017—beyond protein family and domain annotations (2016, background): “The signatures are provided by 14 different member databases: 12 of these are long-standing members of the InterPro Consortium (CATH-Gene3D (3), HAMAP (4), PANTHER (5), Pfam (6), PIRSF (7), PRINTS (8), ProDom (9), PROSITE Patterns (10), PROSITE Profiles (10), SMART (11), SUPERFAMILY (12) and TIGRFAM”
GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank (2017, positive): “InterPro (Mitchell et al. , 2015) combines 14 different protein and domain family databases, including Pfam (Sonnhammer et al. , 1997), CATH-Gene3D (Sillitoe et al. , 2015), CCD (Marchler-Bauer et al. , 2015) and SUPERFAMILY (de Lima et al. , 2010), so covering a large number of protein families, do”