SMART 6: recent updates and new developments

Abstract

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.

Figure 1.

Protein annotation page for Mus musculus phospholipase C, delta 1. More than 600 000 proteins are linked to the KEGG metabolic pathways and orthologous groups, and can be displayed in the interactive Pathways Explorer (12), which provides an interactive, global overview map of the metabolism. Interaction network information has been greatly expanded, and is available for about 2.5 million proteins.

Figure 2.

SMART annotation page for the HDc domain. A new feature of SMART domain annotation pages is the ‘Metabolism’ entry. Based on the mapping of SMART genomic protein database to KEGG orthologous groups, it gives an overview of the domain's presence in various metabolic pathways. Matching pathways are also displayed on the global metabolism overview map (11), with a link to the interactive version, provided by the interactive Pathways Explorer.