[3dem] Welcome to the new PDBe website (pdbe.org)!

Gerard DVD Kleywegt gerard at xray.bmc.uu.se
Thu Aug 5 08:47:31 PDT 2010

PDBe launches its redesigned website (pdbe.org)

The Protein Data Bank in Europe (PDBe; http://pdbe.org) has launched its 
redesigned website with lots of new features, enhancements and improvements. 
This so-called "Midsummer Make-over" is the first in a series of biannual 
upgrades timed to take place around midsummer and midwinter. New features in 
this first make-over include:

- A completely redesigned website with:

   + A tools menu (on the left) that provides access to PDBe services

   + A central panel that allows users to do the most common tasks straight from 
the front page (find various kinds of information about a PDB entry, search by 
a database identifier, or do a sequence search of the PDB)

   + A simple search of *both* PDB and EMDB from the top bar (try a search for 
"Saibil" or "Groel" or "ribosome" to get hits in both databases)

   + Links to go to (quasi-)randomly picked PDB entries (great for teaching and 
demos), accessible from the central panel

- Loads of easy-to-remember shortcuts using the pdbe.org domain name, e.g. 
typing http://pdbe.org in the address bar of your web browser takes you 
straight to the new site, http://pdbe.org/1cbs goes directly to the summary 
page for entry 1CBS, and many more

- A wizard (http://pdbe.org/wizard) to guide novice and non-expert users to the 
information, resource or service they are looking for

- A browser that allows exploration and analysis of the structural archive 
based on biological classifications (implemented to date: EC = 
http://pdbe.org/ec; Pfam = http://pdbe.org/pfam ; and CATH = 
http://pdbe.org/cath ; the browser can also be used to explore the results of 
sequence-similarity searches: http://pdbe.org/fasta)

- PDBprints (c) - a pictorial way of providing at-a-glance information about 
PDB entries - these are used on PDBe summary pages and when displaying the 
results of an advanced search of the PDB (try: 
http://pdbe.org/advancedsearch?text=homeobox ). You can also very easily 
include them in your own web pages. For more information, see 

- Summaries in English for all PDB entries. By default, the first page of each 
PDB entry now contains a user-friendly description of the contents of the entry 
and how the structure was determined (in English sentences) and some useful 
links and images - try http://pdbe.org/1fss or any of your own favourite 
structures (or http://pdbe.org/random for a randomly picked entry)

In addition, there are countless minor tweaks, changes and improvements.

The Protein Data Bank in Europe hopes you will find the new website and 
features useful and looks forward to your comments and suggestions (using the 
'Feedback' form which you will find at the top of each page).


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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