Friday, July 16, 2010

PDB fingerprints make salient features of PDB entries obvious at a glance

In the past couple of days, I have followed with great interest the thread "PDBprints - salient, at-a-glance info about PDB entries" in CCP4BB. The idea behind PDBprints (short for PDB finger prints) is very simple: now with over 66 thousands entries, no one could possibly be intimately familiar with many of the structures in PDB. Yet "it would be very useful to have a way of obtaining at-a-glance information about the salient features of one or more PDB entries." In this scheme, key features (e.g., experimental method, species, protein/NA/ligand components, published or not) are represented by stylized icons called PDBlogos; a set of which organized in a specific order gives PDBprints.

The initial announcement, posted on Thursday by Gerard Kleywegt (the current Director of PDBe), has been well-received by the community. I am very impressed by the quality of the (over a dozen) feedbacks on icons coloring for presence/absence of a feature, and the proper icons for species etc. On the other hand, I am surprised by the quick and concrete response Gerard posted today, addressing the various issues.

Over the years, I have taken PDB/NDB mostly as data repositories; I regularly download (update) nucleic-acid containing structures for local analyses. Among the three wwPDB sites (RCSB, PDBe and PDBj), I've only visited the RCSB site on a regular basis. Now I find more features are available from PDBe, which I will browse more in the future.