SMART: recent updates, new developments and status in 2015

By Ivica Letunic, Tobias Doerks, Peer Bork. Nucleic Acids Res., 2014

1,468 citations recorded by the source corpus.

SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de/) providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures. In the current version, SMART contains manually curated models for more than 1200 protein domains, with ∼200 new models since our last update article. The underlying protein databases were synchronized with UniProt, Ensembl and STRING, bringing the total number of annotated domains and other protein features above 100 million. SMART's ‘Genomic’ mode, which annotates proteins from completely sequenced genomes was greatly expanded and now includes 2031 species, compared to 1133 in the previous release. SMART analysis results pages have been completely redesigned and include links to several new information sources. A new, vector-based display engine has been developed for protein schematics in SMART, which can also be exported as high-resolution bitmap images for easy inclusion into other documents. Taxonomic tree displays in SMART have been significantly improved, and can be easily navigated using the integrated search engine.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0432b705cb745420f552fedf998f79bdcf5049b3

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Citations in the corpus

The genetic landscape of a physical interaction (2018, methodology): “Cloning of FOS and JUN into the plasmid backbone FOS and JUN basic leucine zipper domains, as defined by SMART (Letunic et al., 2015), were amplified from human cDNA provided by Juan Valcarcel using primer pairs OGD098-OGD110 and OGD113-OGD125, respectively.”
The Human Transcription Factors. (2018, neutral): “For example, the simple AT-hook domain (represented by a 13 amino acid [aa] consensus) is predicted to be present in 3 and 21 human genes according to the Interpro and SMART databases, respectively.”
Stress-triggered phase separation is an adaptive, evolutionarily tuned response (2017, background): “de, (Letunic et al., 2015)) on the basis of possessing a specific domain architecture: four RRM domains and a PolyA (poly(A)-binding protein C-terminal) domain, resulting in 742 sequences.”
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015, methodology): “At the taxonomic level of each OG, available functional annotations are collected from many sources including free-text descriptions in source genome databases, COG functional categories (8), Gene Ontology terms (42), KEGG pathways (43) and SMART/Pfam protein domains (44,45).”
20 years of the SMART protein domain annotation resource (2017, background): “new models added since our last update article (1).”
NCBI’s Conserved Domain Database and Tools for Protein Domain Analysis (2019, methodology): “Current Protocols in Bioinformatics by CDD staff along with additional sources from Pfam (Finn et al., 2016), SMART (Letunic et al., 2014), KOG (Tatusov et al., 2003), COG (Tatusov et al., 2001), PRotein K(c)lusters (PRK; Klimke et al., 2009) and TIGRFAMs (Haft et al., 2013)—at an E - value threshol”
YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs (2017, background): “We further analyzed this system using both N- and C-terminal constructs of YTHDC1, both of which feature several distinct regions of predicted low complexity (Letunic et al., 2015).”
Consensus protein design (2016, methodology): “The most efficient way to acquire sequences is via sequence alignment databases such as Pfam (Sonnhammer et al., 1998; Finn et al., 2016), Prosite (Sigrist et al., 2013), SMART (Letunic et al., 2015) and Superfamily (Wilson et al., 2009).”