Hi all,
Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org) releases
new, improved and updated versions of its tools and resources. Below is a
brief description of new features and services that have been released this
summer (or what passes as summer in the UK). As always, the URL
http://pdbe.org will take you to the PDBe website. Many of the features can be
accessed through the "PDBe Tools" menu on the left side of the front page, or
you can use the shortcut URLs mentioned below.
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The executive summary for the busy PI:
#1. Slice viewer for tomograms in EMDB
#2. Improved analysis and validation of NMR entries
#3. Enhanced FASTA browser for the PDB archive (http://pdbe.org/fasta)
#4. New features on some PDB entry pages
#5. Weekly release history for PDB entries, EMDB entries and PDB compounds
(http://pdbe.org/latest)
#6. Advanced SQL queries for power-users (http://pdbe.org/sqldemo)
And many other smaller (or "under-the-hood") improvements.
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The nitty-gritty details for the eager structure user:
#1. Slice viewer for tomograms in EMDB
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The major piece of new functionality is a slice viewer for tomograms in EMDB.
The viewer, developed in collaboration with the Open Microscopy Environment
(OME), works within the context of most common web browsers and does not
require any installation of software locally. To access the slice viewer for a
particular EMDB entry, e.g. emd-1053, navigate to the entry page, in this case
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.
#2. Improved analysis and validation of NMR entries
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Vivaldi (http://pdbe.org/vivaldi), our interactive server for display,
analysis and validation of NMR entries (including experimental data and
violations, where available), has been improved and enhanced, thanks in part
to user feedback. New types of data and analysis include angular restraints
and their violations and circular variance plots for main-chain torsions. You
can view your favourite NMR entry by using a shortcut URL such as
http://pdbe.org/vivaldi/2k4v or from the main Vivaldi page. If you're not an
expert in NMR and feel intimidated by ensembles and distance restraints, take
Vivaldi for a spin!
PDBe also generates OLDERADO pages for NMR ensembles
(http://pdbe.org/olderado) - these show useful information about rigid domains
and clusters of models in the ensemble. Where non-experts often take "MODEL 1"
from an ensemble for display, molecular replacement, docking, homology
modelling etc., OLDERADO will tell you which model is most representative.
These pages are accessible from the OLDERADO start page, or directly, e.g.
http://www.ebi.ac.uk/pdbe-apps/nmr/olderado/searchEntry?pdbCode=2k4v. Note how
the colouring of the rigid domains and cluster representatives is repeated in
the tables to make identification easy. There are also buttons to launch
Vivaldi showing the same information in 3D.
The "Experiment" pages for NMR entries (e.g.,
http://pdbe.org/2k4v/experimental) link to both OLDERADO and Vivaldi (among
many other things).
#3. Enhanced FASTA browser for the PDB archive
----------------------------------------------
PDBe offers a number of (PDBeXplore) browsers that allow analysis of the
archive based on a variety of biological and chemical classification systems
(EC code, Pfam family, GO classifications, taxonomy, etc. - see
http://pdbe.org/pdbexplore). One of these browsers allows you to study all PDB
entries that contain proteins that show sequence similarity to a protein of
your interest (as identified by a FASTA search; http://pdbe.org/fasta). This
browser has now been improved and can take UniProt and PDB identifiers as
input to retrieve sequences itself - after providing one of these identifiers,
the "Fetch sequence" button will retrieve the sequence (if it can find it) and
put it in the sequence box. After that, change the E-value and/or %-identity
cut-off and hit "Submit" to retrieve any and all hits in the PDB. In addition,
there is a new tab in the browser panel ("Unreleased entries") that shows any
hits to proteins found in PDB entries that have not yet been released but
whose sequences are public.
#4. New features on some PDB entry pages
----------------------------------------
PDB entry pages can be accessed quickly with URLs like http://pdbe.org/1cbs.
For some time now, we have provided links to corresponding PDB_REDO pages
(http://www.cmbi.ru.nl/pdb_redo/), but these have been somewhat hard to find.
Now, when PDB_REDO has data about an X-ray entry, we provide an explicit link
on the downloads page of that entry, e.g. http://pdbe.org/1cbs/downloads shows
a link to http://www.cmbi.ru.nl/pdb_redo/cb/1cbs/index.html.
Some ligands are made up of smaller parts that are also present in the PDB
chemical components dictionary. In such cases, we now show these explicitly on
the ligands page of the corresponding PDB entry, for example:
http://pdbe.org/1the/ligands.
For PDB entries that have not yet been released, but for which the sequence
information is public, we now show each sequence and provide a link "Related
PDB sequences" to the FASTA browser (see item #4 above) so you can find out in
seconds if it is related to any proteins already in the public archive (or
other unreleased entries, e.g. complexes or competitors' structures). To find
examples of unreleased entries, you can use http://pdbe.org/status (at the
time of writing, entry 4auc is a working example: http://pdbe.org/4auc).
#5. Weekly release history for PDB entries, EMDB entries and PDB compounds
--------------------------------------------------------------------------
PDBe offers a weekly overview of newly released, revised and removed PDB
entries (http://pdbe.org/latest), PDB compounds and EMDB entries. We have now
added a history function so that, if you have been away for a week or more,
you can quickly catch up. The previous week's release is available from a
drop-down menu - older releases (back to 30 March 2011) can be selected using
a calendar tool.
#6. Advanced SQL queries for power-users
----------------------------------------
Advanced users who are familiar with the database-querying language SQL (and
with the PDBe search database) can perform many powerful queries that cannot
(easily) be done using standard search services. To help these users, we have
collected some example queries. They can be executed through the PDBe database
browser and modified to experiment or to tailor it to your specific needs.
Surf to: http://pdbe.org/sqldemo
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PDBe maintains a list of publications (co-)authored by PDBe staff (at
http://pdbe.org/publications). If you would like to read more about PDBe
services, our paper in the 2012 Databases issue of NAR (Nucleic Acids
Research) is highly recommended - open access is provided here:
http://nar.oxfordjournals.org/content/40/D1/D445
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
gerard from ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_admin from ebi.ac.uk
