Hi all,
As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org)
announced a substantial make-over of its website last summer, including the
release of a number of new features (such as PDBprints -
http://pdbe.org/pdbprints - and a biologist-friendly structure browser -
http://pdbe.org/browse). Now we are proud to announce a further update which
brings several new tools and services as well as lots of improvements "under
the hood" (performance, presentation, search speed, etc.).
As always, the URL http://pdbe.org will take you to the PDBe website.
- One of the first things you'll probably notice is a protein structure on the
right. This is an appetiser for a new feature called "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 users to delve a bit deeper using one or more
PDBe resources. Try it out at: http://pdbe.org/quips
- If you look at the left of the front page, you'll find three new options at
the top of the PDBe Tools menu - these give you quick access to the latest PDB
and EMDB entries and (uniquely, we think) to new or revised chemical compounds
in the PDB. The results are presented in a fresh new way (as opposed to a
simple table or list) where each entry or ligand comes with annotation, an
image, and buttons that take you to related pages or that launch PDBe services
for that particular entry or compound. Give it a go at: http://pdbe.org/latest
- Speaking of chemical compounds in the PDB, the biologist-friendly structure
browser (a.k.a. PDBeXplore) now has a new module that allows browsing and
analysis of all entries that bind a certain chemical compound. Try it out with
your favourite compound (or try ATP) at: http://pdbe.org/compounds (By the
way, all the previous browser modules have undergone significant improvements
and speed-up.)
- We have begun to incorporate or emulate some of the functionality offered by
our colleagues at PDBsum. For example, our enzyme browser
(http://pdbe.org/enzymes) now lists for every EC class you select how many
structures there are in the PDB for that class. In this release of the website
we also introduce PDBsum-inspired "PDB highlights", e.g. the oldest entries in
the current release, the highest resolution crystal structures, the longest
protein chains, etc. You can find them here: http://pdbe.org/highlights
- Searches of the PDB and EMDB from the search box in the top bar of the PDBe
front page have also been improved and the results are now presented in the
same way as the latest entries and the highlights. You can also type the name
of a PDBe service (such as pdbefold or pdbepisa) in the search box and the
system will take you to the appropriate page. The search box is available on
the front page at http://pdbe.org/ (or if you just want to see a quick
example, with hits in both PDB and EMDB, try:
http://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term=baumeister)
- We introduce a new widget called PDBportfolio that we hope will soon be in
widespread use on webpages everywhere (for instance:
http://xray.bmc.uu.se/gerard/structures_pdbportfolio.html). For one or more
PDB entries, PDBportfolio presents an annotated slideshow consisting of
informative images, annotation and links for further information or
exploration. Categories of information covered (in this first release of the
widget) include the quaternary structure, contents of the deposited entry,
Pfam/CATH/SCOP domain mappings on the structure, binding environment of one or
more ligands and experiment-related information. To read more about this
widget, go to: http://pdbe.org/portfolio PDBportfolio is already in use at the
Uppsala Electron-Density Server, e.g.:
http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs
- Our PDB Atlas pages have also been improved. The summary pages include the
PDBportfolio widget discussed above (e.g.: http://pdbe.org/1cbs) and you can
now launch protein-sequence searches of the entire PDB directly from the
primary structure pages (e.g.: http://pdbe.org/1fss/primary) - simply click on
the friendly green button labelled "Related PDB sequences". Further, we now
provide Atlas pages for all possible PDB codes. If an entry is not in the
current release of the archive, a message will be displayed that informs you
about its status (e.g., theoretical model, superseded entry, deposited but not
yet released entry, etc.) An example: http://pdbe.org/2y8d
- On the front page (under the "About us" tab) we now maintain a list of
upcoming events in which PDBe staff will participate (roadshows, conferences,
etc.). If you should participate in an event on this list, come and say hello!
If you are interested in attending a roadshow from the list, get in touch. A
shortcut to this page is: http://pdbe.org/events
- PDBe is now on Facebook. To get the latest PDBe updates in your Facebook
news feed, simply "like" us -
http://www.facebook.com/pages/Protein-Data-Bank-in-Europe-PDBe/153011668068957
- Finally, in January's Database issue of Nucleic Acids Research you can find
an article describing recent developments and future plans of the Protein Data
Bank in Europe - you can read or download the paper here:
http://nar.oxfordjournals.org/content/39/suppl_1/D402
--Gerard
---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
