SMART 7: recent updates to the protein domain annotation resource

By Ivica Letunic, Tobias Doerks, Peer Bork. 2011

1,669 citations recorded by the source corpus.

SMART (Simple Modular Architecture Research Tool) is an online resource (http://smart.embl.de/) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 7 contains manually curated models for 1009 protein domains, 200 more than in the previous version. The current release introduces several novel features and a streamlined user interface resulting in a faster and more comfortable workflow. The underlying protein databases were greatly expanded, resulting in a 2-fold increase in number of annotated domains and features. The database of completely sequenced genomes now includes 1133 species, compared to 630 in the previous release. Domain architecture analysis results can now be exported and visualized through the iTOL phylogenetic tree viewer. ‘metaSMART’ was introduced as a novel subresource dedicated to the exploration and analysis of domain architectures in various metagenomics data sets. An advanced full text search engine was implemented, covering the complete annotations for SMART and Pfam domains, as well as the complete set of protein descriptions, allowing users to quickly find relevant information.

Subfields: Molecular Biology

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Citations in the corpus

The InterPro protein families database: the classification resource after 15 years (2014, background): “From an initial core of four source databases (Pfam (1), PRINTS (2), PROSITE (3) and ProDom (4)), InterPro has expanded, so that it now integrates signatures from seven additional repositories: CATH-Gene3D (5), HAMAP (6), PANTHER (7), PIRSF (8), SMART (9), SUPERFAMILY (10) and TIGRFAMs (11).”
The eukaryotic linear motif resource ELM: 10 years and counting (2013, background): “In addition, links have been provided to Pfam (25) or SMART (26), where more detailed information about the respective domain can be found.”
SMART: recent updates, new developments and status in 2015 (2014, background): “Here we give an overview of the major developments and new features introduced since our last update (6).”
STRING v9.1: protein-protein interaction networks, with increased coverage and integration (2012, background): “…node in the network shows a preview to 3D structural information, if available, and can be clicked to reveal a pop-up window with more information about the protein [including its annotation (58), SMART domain-structure (59), structure homology models from SWISS-MODEL Repository (60), etc.].”
CDD: conserved domains and protein three-dimensional structure (2012, methodology): “The majority of protein domain models collected in databases such as Pfam (1) and SMART (2), the contents of which have been incorporated into Conserved Domain Database (CDD), stem from the results of such sequence analyses, and the CDD in-house curation effort has adopted a similar view of protein ”
eggNOG v4.0: nested orthology inference across 3686 organisms (2013, methodology): “Visualization of the precomputed phylogenetic trees is also provided via iTOL (68) and can be viewed with the assigned PFAM (47) and SMART (46) domains.”
InterProScan 5: genome-scale protein function classification (2014, methodology): “As InterProScan 5 makes use of the Hibernate object-relational mapping tool (http://www.hibernate.org/), it should be possible to port the back-end to run on most relational database management systems.”