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. 2006 Jan 1;34(Database issue):D257-60.
doi: 10.1093/nar/gkj079.

SMART 5: Domains in the Context of Genomes and Networks

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Free PMC article

SMART 5: Domains in the Context of Genomes and Networks

Ivica Letunic et al. Nucleic Acids Res. .
Free PMC article

Abstract

The Simple Modular Architecture Research Tool (SMART) is an online resource (http://smart.embl.de/) used for protein domain identification and the analysis of protein domain architectures. Many new features were implemented to make SMART more accessible to scientists from different fields. The new 'Genomic' mode in SMART makes it easy to analyze domain architectures in completely sequenced genomes. Domain annotation has been updated with a detailed taxonomic breakdown and a prediction of the catalytic activity for 50 SMART domains is now available, based on the presence of essential amino acids. Furthermore, intrinsically disordered protein regions can be identified and displayed. The network context is now displayed in the results page for more than 350 000 proteins, enabling easy analyses of domain interactions.

Figures

Figure 1
Figure 1
Prediction of catalytic activity in SMART. First guanylyl cyclase domain in human adenylate cyclase type III (ENSP00000260600) is marked as ‘inactive’ because the two amino acids required for its activity are not present. Domain annotation page shows which amino acids are not detected and gives pointers to the relevant literature.
Figure 2
Figure 2
Interaction networks in SMART. Around 350 000 protein annotation pages include an interaction network in a pop-up window. Networks are linked to the STRING database () which provides the data.
Figure 3
Figure 3
Taxonomic trees in SMART. (a) Domain architecture query results grouped into a tree. Users can select individual proteins or taxonomic nodes to display. (b) Domain annotation pages show detailed domain and protein counts in various taxonomic nodes.

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