[3dem] Introducing one-click access to PDB data at PDBe

Gerard DVD Kleywegt gerard at xray.bmc.uu.se
Thu Aug 5 08:51:24 PDT 2010

Introducing one-click access to PDB data at PDBe

When you visit the newly redesigned home page of the Protein Data Bank in 
Europe (PDBe; http://pdbe.org/), the panel in the centre of your screen 
(labelled "Home") provides one-click access to PDB data (tab labelled "Quick 
access"). Together with the "PDBe Tools" menu on the left this covers the large 
majority of actions users tend to carry out.

For the following, first throw your browser at: http://pdbe.org/

One-click access

The "Quick access" tab consists of three parts. The top one enables you to type 
a PDB code and then click one of six buttons to immediately get to important 
information about that entry:
   - Entry summary - takes you to the new English-language summary page for that 
entry at PDBe
   - Download PDB file - takes you directly to the PDB file of the entry
   - Download other files - takes you to a page with links to files related to 
that entry (e.g., mmCIF and PDBML files of the structure, experimental data, 
SIFTS data, and PDBePISA quaternary structure files)
   - Quaternary structure - takes you to a page with information about the 
probable quaternary structure (from PDBePISA)
   - Similar structures - runs the PDBe structure-similarity server for that 
entry (PDBeFold, based on the program SSM)
   - Motifs and sites - takes you to a page with more information about sequence 
motifs, 3D motifs, ligand interactions, and much more (PDBeMotif)

Quick search by external database identifier

The middle part of the "Quick access" tab allows you to search for PDB entries 
based on some external database identifier (e.g., from PubMed, UniProt or 
SCOP). For example, if you enter UniProt ID P29373 you will be presented with a 
table with (today) 30 hits.

Random entries - more useful than you would think

The bottom part of the "Quick access" tab we find to be extremely useful for 
teaching, tutorials and demonstrations (or for when you just want to kill a few 
minutes looking at random PDB entries). It consists of a number of links, each 
of which will give you a random PDB entry (optionally, satisfying a criterion 
pertaining to the method used to solve the structure, the type of molecules in 
the entry, or when the entry was released). Looking for an(y) entry from the 
1970s? Looking for an(y) example of a structure solved by hybrid methods? 
Looking for an(y) intact virus? Thanks to these links, finding one is only a 
mouse-click away.

Say that you are writing an assignment for students in which they have to work 
with a protein-DNA complex. Instead of letting them all work on the same PDB 
entry (or let them pick from a list which may include entries that get 
superseded or obsoleted in the future), you can now just tell them to get a 
randomly picked one.

Quick sequence searches

Below the "Quick access" tab, you will notice another tab called "Sequence 
search". This is our one-stop shop for FASTA searches against the sequences of 
all proteins in the PDB (tip: try out the option to analyse the results in the 
PDBe browser!). We will add some more bells and whistles in the future.

PDBe features

Finally, the "PDBe feature" tab presents you with a short description of a 
randomly picked PDBe resource, tool or service. (The database of PDBe-feature 
descriptions is still small but we are adding to it.) Who knows? We might offer 
something you need and didn't know about.


As always, we welcome comments and suggestions on these new features 
(preferably using the big, fat "FEEDBACK" button on the PDBe web pages).


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

More information about the 3dem mailing list