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Jan 15, 2013 (Vol. 33, No. 2)


  • Includes glossary, two different operating modes
  • No user guide

If you are interested in studying protein domains—their phyletic distributions, functional class, important amino acid residues, etc.—then it would be a “smart” move to visit the website for the Simple Modular Architecture Research Tool (SMART). Originally described in a 1998 publication, this tool is still very actively updated, with the most recent publication related to SMART being published this year. Through its ability to identify modular domains from user-inputted protein sequences or sequence IDs, SMART is a great tool for scientists interested in the analysis of protein domain architecture. SMART can be used in two modes: normal or genomic. Whereas the normal mode includes various proteome sources in its database, the genomic mode only includes the proteomes of completely sequenced genomes. The site includes a glossary to familiarize users with some of the jargon they might encounter when using SMART, such as “HMM consensus” and “seed alignment.”

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*The opinions expressed are solely those of the author(s) and should not be construed as reflecting the viewpoints of the publisher, Genetic Engineering & Biotechnology News, Mary Ann Liebert, Inc., the publishing house, or employees and affiliates thereof.

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Scientifically Studying Ecstasy

MDMA (commonly known as the empathogen “ecstasy”) is classified as a Schedule 1 drug, which is reserved for compounds with no accepted medical use and a high abuse potential. Two researchers from Stanford, however, call for a rigorous scientific exploration of MDMA's effects to identify precisely how the drug works, the data from which could be used to develop therapeutic compounds.

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