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Nov 15, 2007 (Vol. 27, No. 20)

BindingMoad.org – The Mother of All Databases

  • Database info
  • Vanilla interface
You’ve got to admire the moxie of the designers of this site. The Mother Of All Databases is a title that is pretty much impossible to live up to, but that doesn’t stop them from trying. Organized to provide visitors access to ligand-protein binding (that seems to be the theme this month) data from PDB, the organizers have chosen to create yet another subset of PDB. Their requirements for inclusion in the listings include 1) well resolved structure (2.5 angstroms or better); 2) biologically relevant ligands; and 3) data extracted from the literature. Searching options include a standard search engine and a browsing option. The latter is useful for looking through enzyme classes for relevant data. Specifiable search criteria in the search engine include PDB code, keywords, source, ligand, author surname, and maximum/minimum resolution, among others. While it is not truly the Mother Of All Databases, it is in fact a useful database for protein binding data.
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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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