Introducing one-click access to PDB data at PDBe
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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
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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
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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
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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
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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
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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.
Feedback
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As always, we welcome comments and suggestions on these new features
(preferably using the big, fat "FEEDBACK" button on the PDBe web pages).
--Gerard
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Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
