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[X-plor] PDBe introduces Quips - QUite Interesting PDB Structures

Gerard DVD Kleywegt via x-plor%40net.bio.net (by gerard from xray.bmc.uu.se)
Fri Mar 25 13:43:38 EST 2011

Hi all,

As part of its recent winter update, the Protein Data Bank in Europe (PDBe; 
http://pdbe.org) introduced Quips - "QUite Interesting PDB Structures". Quips 
are short stories about one or more interesting or topical structures, coupled 
with an interactive viewer and often a tutorial that allows you to do more 
detailed exploration of a structure using PDBe resources. Try it out at: 

Perhaps you have come across macromolecular structures in paper figures and on 
journal covers but would like to delve deeper into the structures that 
interest you? We hope that Quips will be a starting point for further 
exploration of structures in the PDB archive and will (help you) answer 
questions about structural data.

Quips are short articles and tutorials on structures picked from the PDB 
archive. More often than not, as the name suggests, these articles will focus 
on "quite interesting" PDB structures rather than daunting behemoths. The 
tutorials assume that you have a background in biology, chemistry or medicine 
and have an interest in proteins, nucleic acids and ligand interactions. New 
Quips will be added approximately once a month. They are currently produced by 
PDBe annotation staff, but we would be more than happy to host Quips produced 
by structural biologists who would like to "sell" their own structures (or 
even someone else's).

Quips articles include interactive structure displays with a number of 
predefined (often animated) views to highlight points made in the text. Follow 
the tour of each structure by clicking on links to these views and they will 
appear, in real time, in the molecular viewer window. The viewer is also yours 
to command in case you want to spin the structure around or go on a detour to 
a different part of the structure. Afterwards simply rejoin the Quips tour by 
selecting the next "view" link. For more information about the user-interface, 
see http://pdbe.org/quips

Some Quips will also introduce you to PDBe resources and services that can be 
useful in your own explorations of the wonderful world of structures. When a 
particular PDBe service is especially useful for understanding a Quips 
structure, we will provide a walk-through to show you how it works. This will 
get you started in using these services for your own structural searches and 

Our inaugural Quips (of 14 February ...) was entitled "A deadly toxin with a 
romantic name: Panton-Valentine Leukocidin complex" and was accompanied by a 
tutorial on how to use PDBeFold (a.k.a. SSM) to compare the structures of two 
PVL components and superimpose them on alpha-hemolysin. This Quips can be 
found at http://pdbe.org/quips?story=PantonValentine

Our March Quips commemorates the fact that it is 20 years ago that the 
structure of Nerve Growth Factor (NGF) was determined. The accompanying 
tutorial shows you how to use PDBePISA to analyse the quaternary structure of 
NGF. To access this Quips, go to: http://pdbe.org/quips?story=NGFstory

If you would like to use the Quips format to tell a story about any 
interesting structures of your own then please get in touch!

We welcome your comments, bug reports and feature requests on Quips. Please 
use the feedback button at the top of any PDBe web page.


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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