[3dem] EMsearch - a powerful new search tool for EMDB data

[Ardan Patwardhan]

Dear All,

 

The Protein Data Bank in Europe (PDBe; http://pdbe.org) is proud to
introduce EMsearch (pdbe.org/emsearch), an advanced search tool for the EMDB
archive. The functionality of EMsearch is a superset of (and replacement
for) what has been provided by previous search tools for the EMDB archive on
our site.

 

EMsearch presents a rich set of search criteria, including EMDB codes,
fitted PDB codes, authors, keywords, resolution, molecular weight,
aggregation state, status, key dates, citations, software package and
microscope. Search criteria with a controlled vocabulary, such as EMDB
status or software package, are accessible on the search form as collapsible
panels with check-boxes rather than as cumbersome drop-down lists; this
makes the selection of multiple items much easier. For a number of criteria
you may use wildcards (e.g., authors: saib*), logical operators (e.g.,
authors: saib* AND orl*) and ranges (e.g., EMDB codes: 

[1000 TO 1010]).

 

Top tip: to find all EMDB structures that have models fitted to them, enter
[0 TO 9ZZZ] in the Fitted PDB codes box!

 

The information that is to be shown in the search results can be customised
using the "Configure search results" > "Output information" 

panel. Press the "Submit" button and the results will appear in a new
browser tab. You can change the number of results shown per page and the
sort order. For each entry, links and buttons provide quick access to
entry-summary pages, associated EMDB entries, fitted PDB models and
citations. You may download the results as a tab-delimited text file or as
an XML file.

 

EMsearch is implemented as Javascript widgets that can be integrated into
external web pages. For instance, you could use these widgets on your own
web pages to show a list of the latest ribosome entries in EMDB or the most
recent EMDB entries from your lab. The information shown will always be
up-to-date!

 

For more information, feedback or help, please do not hesitate to contact us
at emhelp at ebi.ac.uk.

 

 

Ardan Patwardhan, 

EMBL-EBI

Hinxton, Cambridge CB10 1SD, UK
Tel: +44 1223 492649

ardan at ebi.ac.uk

 

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