Hi all,
The Protein Data Bank in Europe (PDBe; http://pdbe.org) continues to improve
its services to the scientific community. As part of our recent website
update, the EM resources at PDBe (http://pdbe.org/emdb) have been improved.
EMDB (http://emdatabank.org) contains over 1000 maps and is expected to grow
5-10 fold over the next 10 years. The data held in EMDB form a treasure trove
of information on the state of, and trends in, the 3DEM field. Examples of
interesting information that can be mined from the archive are trends in the
resolution obtained using different techniques and comparisons of the relative
popularity of microscopes and software packages. A new service
(http://pdbe.org/emstats) has been developed at PDBe to mine the database for
such information and present the results as interactive charts. The charts are
generated dynamically and represent the current state of the information in
the database. The charts are active, i.e. when clicked, a query is sent to the
database and the results are shown below the charts. Clearly, the current set
of charts represents only a fraction of the interesting information that can
be extracted from the database and we invite the 3DEM community as well as the
wider structural biology community to engage with us in expanding this
service.
Atlas pages for EMDB entries can now be accessed directly using URLs of the
type: pdbe.org/emd-xxxx, where "xxxx" is the 4-digit numerical EMDB accession
code. For example, http://pdbe.org/emd-1831 takes you to the entry "Pig
Gastric H,K-ATPase with bound BeF and SCH28080" by Abe, Tani and Fujiyoshi.
The look and feel of the EMDB atlas pages (served at both EMDataBank sites,
PDBe and RCSB) have also been improved - for instance, empty boxes are not
shown so as to create a cleaner and more concise look and an enhanced version
of the OpenAstexViewer can be accessed from an entry's visualisation page. The
viewer can overlay fitted PDB models on maps (for an example, see
http://pdbe.org/emd-1180) and use symmetry information to generate
symmetry-related copies of models. (See also:
http://www.emdatabank.org/improved_3d_viewing.html)
We hope that you will find the EM resources at PDBe useful. As always, we
welcome constructive criticism, comments, suggestions, bug reports, etc.
through the feedback button at the top of any PDBe web page.
--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
