[3dem] New and improved EMDB search and visualisation services at PDBe

[Ardan Patwardhan]

Dear all,

 

The Protein Data Bank in Europe (PDBe; http://pdbe.org) has made a number of
major improvements to some of its EMDB-related services:

 

* Searching EMDB

 

In keeping with the PDBe motto -"Bringing structure to biology"- we want to
make the EMDB archive more useful to the non-expert biologist. We have
therefore improved our EMDB search service (EMsearch;
http://pdbe.org/emsearch) so that it is now possible to search based on
sample information. For instance, one can search for eukaryotic ribosomes
bound to tRNA (select "Sample" -> "Component type" -> "eukaryotic ribosome"
and "Sample" -> "Nucleic-acid-related options" -> "tRNA") or for viruses
that infect vertebrates (select "Sample" -> "Component type" -> "virus" and
"Sample" -> "Virus-related options" -> "Host category" -> "vertebrates").
The search results now contain sample information, including the taxonomy of
individual components with links to the NCBI Taxonomy Browser.
Unfortunately, the sample information is not uniformly comprehensive for all
EMDB entries because it relies on the depositor's goodwill to provide this
information. However, we hope that the improvements to EMSearch will
encourage depositors to provide more information in the future. Another
improvement of the search results is that they include links to the
corresponding publications based on the DOI. If you wish to link to a
particular search result, you can use the following URL:
http://pdbe.org/emsearch/XXXX, where XXXX is matched against a range of
fields including title, authors, and sample component information. For
instance for groel try http://pdbe.org/emsearch/groel.

 

* EMDB statistics and charts

 

EMstats (http://pdbe.org/emstats) is the PDBe service for easy data-mining
of the current EMDB holdings. A new option "Sample taxonomy statistics for
released maps" has been added. Two charts are displayed: the distribution of
maps among the 12 most common sample species, and the distribution of maps
among the 12 most common virus host categories. As with most of the charts
available from EMstats, you can click on data points to get a list of
corresponding EMDB entries. Based on your feedback, we have further added
charts showing trends and distributions for usage of software packages and
microscopes on the basis of number of publications. These can be contrasted
with the corresponding charts based on the number of released entries that
have been available for some time. The new charts can be viewed as
normalisations of the previous ones, taking into account the fact that one
publication may correspond to multiple EMDB entries.

 

* Slice viewer for tomograms in EMDB

 

This viewer, developed in collaboration with the Open Microscopy Environment
(OME) team in Dundee, works within the context of most common web browsers
and does not require any installation of software locally. The viewer is
only available for entries marked as "individual structure" in the EMDB - a
category including tomograms and sub-tomogram averages. To access the slice
viewer for a particular EMDB entry, navigate to its entry page (for
instance: http://pdbe.org/emd-1053), select the "Visualization" page (from
the menu on the left) and click on "Slice viewer (PDBe)". Hover over the
question mark icon for a brief explanation of options and controls.

 

Many of these new features have been implemented as a direct result of the
feedback provided by members of the EM community - thank you for your
suggestions and please keep them coming!

 

Best wishes

 

Ardan Patwardhan, 

EMBL-EBI

Hinxton, Cambridge CB10 1SD, UK

Tel: +44 1223 492649

ardan at ebi.ac.uk

 

 

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