[X-plor] Introducing PDBprints - salient, at-a-glance info about PDB entries

Gerard DVD Kleywegt via x-plor%40net.bio.net (by gerard from xray.bmc.uu.se)
Thu Jul 15 06:02:17 EST 2010


If you were born before the Dutch lost their first World Cup final, you may 
remember the days when "everybody" knew that PDB entry 1tim was the structure 
of chicken triosephosphate isomerase, 1hhb was human haemoglobin, 1lyz was hen 
egg-white lysozyme, etc. Unfortunately, life for a structural biologist is not 
that simple any longer. Nevertheless, occasionally it would be very handy to 
get at-a-glance information about some of the crucial details of a PDB entry 
or a list of entries.

When the Protein Data Bank in Europe (PDBe; pdbe.org) launched its redesigned 
website recently, we also introduced PDBlogos and PDBprints. PDBlogos are 
stylised, intuitive icons that convey important information about a PDB entry 
(e.g., the experimental technique, the source organism of the sample, or the 
presence of a ligand). PDBprints (short for "PDB fingerprints") are 
collections of PDBlogos displayed in a specific order, where each icon 
represents a well-defined category of information (and where clicking on any 
icon will take you to a webpage with more information about that aspect of the 
PDB entry of interest).

PDBprints are used in a number of places already, e.g.:

- at the top of PDBe's plain-English summary page for every PDB entry (e.g.: 
http://pdbe.org/random)

- in lists of PDBe database-search results (e.g.: 
http://pdbe.org/advancedsearch?text=homeobox)

- at the top of EDS summary pages (e.g.: 
http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1fcc)

A number of other (structural) bioinformatics resources are also considering 
incorporating PDBprints on their webpages. In fact, they are very easy to 
include in *any* webpage as evidenced by this page: 
http://xray.bmc.uu.se/gerard/structures_pdbprints.html

For a five-minute illustrated introduction to PDBprints (including 
instructions on how to include them in your own webpages) point your browser 
to:

                  http://pdbe.org/pdbprints

We hope that you will find PDBprints useful and we value your feedback.


--Gerard

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard from ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin from ebi.ac.uk



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