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  • Web report
  • Open Access

A simple modular architecture research tool for the identification of signaling domains

Genome Biology20001:reports234

https://doi.org/10.1186/gb-2000-1-1-reports234

  • Received: 10 January 2000
  • Published:

Abstract

SMART compares query sequences with its databases of domain sequences and multiple alignments while concurrently identifying compositionally biased regions such as signal peptide, transmembrane and coiled-coil segments.

Keywords

  • Extracellular Domain
  • Query Sequence
  • Domain Sequence
  • Pfam Database
  • Similar Domain

Content

The abstract describing SMART says it best: "SMART compares query sequences with its databases of domain sequences and multiple alignments while concurrently identifying compositionally biased regions such as signal peptide, transmembrane and coiled-coil segments". Annotated and unannotated regions of the sequence can be used as queries in searches of sequence databases. The SMART alignment collection represents more than 250 signaling and extracellular domains. Each alignment is curated to assign appropriate domain boundaries and to ensure its quality. The website contains more than this, however. Each of the domains is carefully annotated, containing information about the proposed role of the domain, a taxonomic breakdown of where the domain is found, links to sequences, three-dimensional structures, primary literature and other databases. In addition, once you have determined the structural organization of the domains in your protein, you can use the SMART website to search for other proteins with the same domains, or use the 'SMART alert' to notify you when similar proteins are deposited in the database.

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Reporter's comments

Timeliness

There is no indication of when the site was last updated.

Best feature

The graphical output, with the underlying HTML links, is a very simple yet powerful method for representing what can be a tremendous amount of information. All the information necessary to determine what each domain does is at the user's fingertips.

Worst feature

It is limited to signaling and extracellular domains and will not find other important domains, including many domains associated with enzymatic functions.

Wish list

It would be more useful if the number of domains represented in the SMART database could be expanded to include more than just signaling and extracellular domains. An option for Postscript output would also be helpful. The GIF output is fine for web pages but it would not take too much effort to make a Postscript version, which would be useful for making figures.

Related websites

Sites for determining protein domains and motifs in proteins include The protein domain database ProDom, The Pfam database of protein domains and HMMs, EMOTIF, Blocks and The protein motif fingerprint database PRINTS.

Table of links

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