I intended to extract protein–chemical links from the PDB (and we wrote this in the paper), but somehow I didn't quite finish the import scripts before we finalized STITCH 1.0. I am sorry about this, and apologize if you are missing interactions.
We are currently preparing the next versions of STRING and STITCH (versions 8 and 2, respectively) and I will import the remediated PDB for the new version. I guess STITCH 2 should come out in Spring 2008.
(Special thanks to Florian Raible for testing his pet molecule and discovering what was missing.)
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