[3dem] Kewl new features on the Protein Data Bank in Europe website - pdbe.org

Gerard DVD Kleywegt gerard at xray.bmc.uu.se
Wed Mar 2 11:18:18 PST 2011

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 

- 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: 

- 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.: 

- 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 - 

- 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: 


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

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