CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

By Aron Marchler-Bauer, Bo Yu, Lianyi Han, Jane He, Christopher J. Lanczycki, Shennan Lu, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales and 12 more. Nucleic Acids Res., 2016

2,488 citations recorded by the source corpus.

NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families. CDD also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures using SPARCLE: Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5699794ad396a965dc382e9e9e8dacc9ddd7fd2b

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Citations in the corpus

PubChem 2019 update: improved access to chemical data (2018, background): “These annotations are collected from major molecular biology databases, including NCBI Gene (12), Gene Ontology (13,14), Human Genome Organization (HUGO) Gene Nomenclature Committee (HGNC) (15), UniProt (16), Protein Data Bank (PDB) (17), Conserved Domains Database (CDD) (18), Pfam (19), MedGen (20)”
GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins (2020, neutral): “Results of the RPS-BLAST searches are processed with rpsbproc utility (28) to generate a map of conserved domains for each RPS-BLAST query.”
CASP13 Target Classification into Tertiary Structure Prediction Categories (2019, methodology): “Sequences corresponding to top templates identified by the Prediction Center (HHpred(11) or LGA(12)) were also submitted as queries against the CDD database.(16) Resulting hits were compared to hits using the target sequences as queries, prioritizing hits from PFAM,(17) but considering hits from alt”
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 2019: improving coverage, classification and access to protein sequence annotations (2018, methodology): “This latter feature is new to In-terPro and enables the representation of concepts such as Pfam clans and CDD superfamilies / collections.”