SMART: recent updates, new developments and status in 2020

By Ivica Letunic, Supriya Khedkar, Peer Bork. Nucleic Acids Res., 2020

1,912 citations recorded by the source corpus.

Abstract SMART (Simple Modular Architecture Research Tool) is a web resource (https://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 9 contains manually curated models for more than 1300 protein domains, with a topical set of 68 new models added since our last update article (1). All the new models are for diverse recombinase families and subfamilies and as a set they provide a comprehensive overview of mobile element recombinases namely transposase, integrase, relaxase, resolvase, cas1 casposase and Xer like cellular recombinase. Further updates include the synchronization of the underlying protein databases with UniProt (2), Ensembl (3) and STRING (4), greatly increasing the total number of annotated domains and other protein features available in architecture analysis mode. Furthermore, SMART’s vector-based protein display engine has been extended and updated to use the latest web technologies and the domain architecture analysis components have been optimized to handle the increased number of protein features available.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/22a630ecd76517a27bbdb7504144f96bc8ad5922

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In Molecular Biology

1. Kai Blin
2. Tilmann Weber
3. Marnix H. Medema
4. Michael A. Fischbach

Citations in the corpus

• antiSMASH 6.0: improving cluster detection and comparison capabilities (2021, methodology): “To identify these biosynthetic functions, antiSMASH uses profile hidden Markov models (pHMMs) from PFAM (26), TIGRFAMs (27), SMART (28), BAGEL (3), Yadav et al. (29), or custom models. antiSMASH 5 contained rules for 58 different BGC types (15), version 6 increases this number to 71.”
• InterPro in 2022 (2022, neutral): “InterPro combines 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),”