CDD/SPARCLE: the conserved domain database in 2020

By Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Gabriele H. Marchler, James S. Song and 7 more. 2019

2,377 citations recorded by the source corpus.

As NLM's Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research. CDD offers both an archive of pre-computed domain annotations as well as live search services for both single protein or nucleotide queries and larger sets of protein query sequences. CDD staff has continued to characterize protein families via conserved domain architectures and has built up a significant corpus of curated domain architectures in support of naming bacterial proteins in RefSeq. These architecture definitions are available via SPARCLE, the Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

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Citations in the corpus

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation (2020, methodology): “The assignment of function to proteins was improved by the addition of the Subfamily Protein Architecture Labeling Engine (SPARCLE(10)) to PGAP for associating curated CDD architectures to proteins.”
COG database update: focus on microbial diversity, model organisms, and widespread pathogens (2020, methodology): “In addition, annotations of approximately 60 COGs were updated to include protein domains from Pfam, InterPro or the NCBI’s Conserved Domain Database (12–14).”
The InterPro protein families and domains database: 20 years on (2020, background): “CDD is a collection of almost 15 000 conserved domain footprints in version 3.17, which is ∼ 2000 signatures more than in version 3.14 (included in In-terPro version 70.0), and SFLD, a smaller scale database, describes structure-function relationships for functionally diverse enzyme superfamilies.”
The Toxoplasma glucan phosphatase TgLaforin utilizes a distinct functional mechanism that can be exploited by therapeutic inhibitors (2022, methodology): “Domains were defined using the NCBI’s Conserved Domain Database (87).”
The Transporter Classification Database (TCDB): 2021 update (2020, background): “YutanpaNet Network-based approach to infer complete multicomponent systems present in (meta)genomes based on the output of getMultiCompSystems. showSubnet Given the output of YutanpaNet, it generates a web-based graphical layout of the subnetwork for an input list of user-specified multicomponent sy”
InterPro in 2022 (2022, positive): “Since our previous publication that described In-terPro 81.0 in 2020 (20), there have been 9 InterPro re-leases, integrating 10 member database updates: CDD (3.18), CATH-Gene3D (4.”