SMART: a web-based tool for the study of genetically mobile domains

By Jörg Schultz, Richard R. Copley, Tobias Doerks, Chris P. Ponting, Peer Bork. Nucleic Acids Res., 2000

1,351 citations recorded by the source corpus.

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Citations in the corpus

Current challenges and best-practice protocols for microbiome analysis (2019, methodology): “These tools and approaches can be classified into four major categories, viz., homology-based, motif- or pattern-based, context-based and other functional predictions: (i) Homology-based tools: This is one of the earliest approaches for which predicted protein sequences are matched to reference prot”
The calpain system. (2003, methodology): “The protease domains of the other molecules (including calpain 2 which is included for comparison) were predicted by the Simple Modular Architecture Research Tool (SMART) (399, 400).”
Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice (2004, methodology): “We found 2210 candidate kinase sequences, 1936 of which contain at least one eukaryotic protein Ser/Thr/Tyr kinase domain based on SMART (Schultz et al., 2000) and Pfam (Sonnhammer et al.”
Rapid automatic detection and alignment of repeats in protein sequences (2000, background): “For every sequence, we veriﬁed that it did not contain a match in SMART.”
Systematic identification of novel protein domain families associated with nuclear functions. (2002, methodology): “A subset of SMART database families represents domains often found in nuclear proteins, as defined by annotation in sequence databases (Schultz et al. 2000).”
InterProScan - an integration platform for the signature-recognition methods in InterPro (2001, methodology): “❖SMART domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues.”
Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. (2001, methodology): “cerevisiae, seven SET domain– containing genes have been identified (Schultz et al. 2000).”
Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. (2000, neutral): “(Schultz et al., 2000) (Figure 2) :”
MUSCLE: a multiple sequence alignment method with reduced time and space complexity (2004, methodology): “Four benchmark datasets have been used to evaluate options and parameters in MUSCLE: BAliBASE [10,11], SABmark [15], SMART [16-18] and our own benchmark, PREFAB [2].”
Predicting subcellular localization of proteins using machine-learned classifiers (2004, methodology): “A domain projection technique based on SMART domains (Schultz et al., 2000), which are included in Interpro, has been somewhat successful in identifying the labels: extracellular, cytoplasmic and nuclear (Mott et al., 2002).”