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[X-plor] A little bit of sunshine from the Protein Data Bank in Europe (pdbe.org)

Gerard DVD Kleywegt via x-plor%40net.bio.net (by gerard from xray.bmc.uu.se)
Thu Jul 12 19:53:04 EST 2012

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.


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 

#6. Advanced SQL queries for power-users (http://pdbe.org/sqldemo)

And many other smaller (or "under-the-hood") improvements.


The nitty-gritty details for the eager structure user:

#1. Slice viewer for tomograms in EMDB
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
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: 
   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


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: 

As always, we welcome constructive criticism, comments, suggestions, bug 
reports, etc. through the feedback button at the top of any PDBe web page.


Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard from ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam  pdbe_admin from ebi.ac.uk

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