SMART 6: recent updates and new developments

By Ivica Letunic, Tobias Doerks, Peer Bork. Nucleic Acids Res., 2008

1,013 citations recorded by the source corpus.

Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains. It provides a user-friendly platform for the exploration and comparative study of domain architectures in both proteins and genes. The current release of SMART contains manually curated models for 784 protein domains. Recent developments were focused on further data integration and improving user friendliness. The underlying protein database based on completely sequenced genomes was greatly expanded and now includes 630 species, compared to 191 in the previous release. As an initial step towards integrating information on biological pathways into SMART, our domain annotations were extended with data on metabolic pathways and links to several pathways resources. The interaction network view was completely redesigned and is now available for more than 2 million proteins. In addition to the standard web access to the database, users can now query SMART using distributed annotation system (DAS) or through a simple object access protocol (SOAP) based web service.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1976758bb45459f8f70df574420322d4774b642b

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Citations in the corpus

A protocol for exosome isolation and characterization: evaluation of ultracentrifugation, density-gradient separation, and immunoaffinity capture methods. (2015, methodology): “Protein sequence analysis of exosome proteins is performed to identify significantly enriched domains/motifs using SMART [30].”
A census of human RNA-binding proteins (2014, background): “InterPro, and currently missed by protein domain annotations (Apweiler et al., 2001; Finn et al., 2010; Letunic et al., 2009).”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, background): “Apart from making the entire SQL database back-end available for download (free for non-proﬁt institutions), this is mainly achieved via the following routes: First, the database maintains mutual HTML cross-references with a number of widely used websites, including UniProt (48), SMART (49), GeneCar”
ELM—the database of eukaryotic linear motifs (2011, methodology): “The ELM resource employs a structural filter (18) to highlight and mask secondary structure elements, as well as SMART (19) to detect protein domains.”
MicrobesOnline: an integrated portal for comparative and functional genomics (2009, methodology): “FastBLAST and FastHMM (13) are used to search against the TIGRFAM (14), Superfamily (15), SMART (16), Pfam (17), Panther (18), PirSF (19), Gene3D (20), COG (21), PDB (22) and UniProt (23) databases.”
SMART 7: recent updates to the protein domain annotation resource (2011, methodology): “Since these are inherently highly redundant, SMART implements a per-species clustering method (7) to minimize the redundancy in the final database.”
CD-HIT Suite: a web server for clustering and comparing biological sequences (2010, neutral): “Received on September 17, 2009; revised on December 7, 2009; accepted on January 2, 2010”
SMART: recent updates, new developments and status in 2015 (2014, methodology): “To minimize the impact of the inherently high redundancy of these databases, we use a per-species clustering method described in (9), which created 1.”
InterPro in 2011: new developments in the family and domain prediction database (2011, methodology): “The InterPro database integrates predictive models, or signatures, from multiple, diverse source repositories: Pfam (1), PRINTS (2), PROSITE (3), SMART (4), ProDom (5), PIRSF (6), SUPERFAMILY (7), PANTHER (8), CATHGene3D (9), TIGRFAMs (10) and HAMAP (11).”
Specificity of polysaccharide use in intestinal Bacteroides species determines diet-induced microbiota alterations (2010, neutral): “The SMART predicted BT1754 domain boundaries are shown below the sequence (http://smart.embl-heidelberg.de/) (Letunic et al., 2009).”
20 years of the SMART protein domain annotation resource (2017, methodology): “To minimize the impact of the inherently high redundancy of these databases, we use a per-species clustering method described in (18), which created 2.9 million multi protein clusters with a total of 5.5 million proteins.”
Phospho.ELM: a database of phosphorylation sites—update 2011 (2010, background): “In addition to providing more evidence about the structural properties of the region surrounding the phosphosites, we determine if the sites reside within domains annotated in the SMART resource (42).”
Structure and function of WD40 domain proteins (2011, neutral): “the human genome, there exist 349 WD40 domain containing proteins based on SMART database ( Letunic et al., 2009 ), and this number should be very conservative considering the difficulties in identifying WD40 domains due to the low sequence conservation.”