20 years of the SMART protein domain annotation resource

By Ivica Letunic, Peer Bork. 2017

1,735 citations recorded by the source corpus.

Abstract SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 8 contains manually curated models for more than 1300 protein domains, with approximately 100 new models added since our last update article (1). The underlying protein databases were synchronized with UniProt (2), Ensembl (3) and STRING (4), doubling the total number of annotated domains and other protein features to more than 200 million. In its 20th year, the SMART analysis results pages have been streamlined again and its information sources have been updated. SMART’s vector based display engine has been extended to all protein schematics in SMART and rewritten to use the latest web technologies. The internal full text search engine has been redesigned and updated, resulting in greatly increased search speed.

Subfields: Molecular Biology

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Citations in the corpus

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit (2020, methodology): “Such databases are, for example, the Pfam (El-Gebali et al., 2019), CDD (Lu et al., 2020), and SMART (Letunic & Bork, 2018) domain databases; the SCOPe (Fox et al., 2014) and ECOD (Cheng et al., 2014) structural classification databases; the Protein Data Bank (Berman et al., 2000); and proteomes of ”
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, methodology): “Orthologous Groups were functionally annotated using updated versions of Gene Ontology (36), KEGG pathways (37), SMART/PFAM domains (38) and expanded to CAZy (39) and KEGG modules.”
FlyBase 2.0: the next generation (2018, methodology): “Protein domain information has been enhanced with a new track that shows domains predicted by SMART, supplementing the previously implemented ‘Pfam’ track, and providing a second independent view of which protein domains are encoded by a gene and how they are distributed among exons (7,8).”
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities (2020, background): “75 of SUPERFAMILY (18), version 01 06 2016 of SMART (19) and version 4.”
CDD/SPARCLE: the conserved domain database in 2020 (2019, positive): “17 is the live production version with 52,910 protein- and protein domainmodels obtained from Pfam (1), SMART (2), the COGs collection (3), TIGRFAMS (4), the NCBI Protein Clusters collection (5), NCBIfam (6) and CDD’s in-house data curation effort (7).”
Ensembl 2020 (2019, background): “Variants co-located with a transcript can be displayed and coloured according to their SIFT (41) or PolyPhen-2 (42) predicted pathogenicity alongside exon boundaries and protein domains from Gene3D (43), Smart (44), Pfam (45) and Panther (46).”
The InterPro protein families and domains database: 20 years on (2020, background): “InterPro integrates 13 protein signature databases into one central resource: CATH-Gene3D (1), the Conserved Domains Database (CDD) (2), HAMAP (3), PANTHER (4), Pfam (5), PIRSF (6), PRINTS (7), PROSITE Patterns (8), PROSITE Profiles (8), SMART (9), the Structure–Function Linkage Database (SFLD) (10)”
SMART: recent updates, new developments and status in 2020 (2020, background): “Here we summarize the major changes and new features that have been introduced since our last report (1).”
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets (2020, background): “The commonly available frameworks are: Gene Ontology annotations (all three GO domains) (45), KEGG pathways (41), UniProt keywords (48), Reactome pathways (42), Pfam (49) and SMART (50) protein domains and InterPro protein features (51).”
Design of a specific peptide against phenolic glycolipid-1 from Mycobacterium leprae and its implications in leprosy bacilli entry (2022, methodology): “LAMA2 was scanned for domain and functional motifs in SMART and visualised in the DOG program.(17,18) The DISULFIND server (http://disulfind.”
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018, methodology): “Signatures that represent the same biological entry are integrated together into individual InterPro entries, reducing redundancy (e.g. the CDD, PROSITE Profile, Pfam and SMART signatures representing the CUB domain (cd00041, PS01180, PF00431, SM00042, respectively) are integrated into a single Inte”