October 1, 2008 (Vol. 28, No. 17)
URL:
http://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html
Rating:
Strong Points: Structural data, images
Weak Points: Poor description of content
Summary:
Just when I thought I’d seen all the major iterations of information in the Protein Data Bank (PDB), along come Het-PDB Navi. How’s that for an uninformative, techie name? Described on the opening page of its website as “a navigator of small molecules in PDB,” the site’s name comes from the phrase “heterogen atoms,” whatever those are. As described in the site, they include ligands, cofactors, and other molecules that interact with proteins. Considering that virtually every molecule in a living cell arises as a result of an interaction with a protein (enzymes), I’m still left wondering what they’re talking about. In any event, Het-PDB appears to contain over 8,000 heteroatoms. As one might expect, one can view structures and get structural data downloads from the site. I wasn’t especially impressed with the opening animation inasmuch as it didn’t show anything except spinning molecules and the associated spinning enzymes that bound them. Whoopee. The actual images are worthwhile, however.
