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