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[X-plor] Winter wotsits 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)
Fri Feb 3 14:46:07 EST 2012

Hi all,

The Protein Data Bank in Europe (PDBe; http://pdbe.org) releases new, improved 
and updated versions of its tools and resources twice a year. Now it's time 
for the winter update. Below is a brief description of new features and 
services. 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 


The executive summary for the busy PI:

#1 - A browser of the PDB archive based on GO, the Gene Ontology 

#2 - A service to investigate the status of any PDB entry code ever released 

#3 - New and improved modules to carry out advanced analyses of the PDB 
archive with a very simple interface (http://pdbe.org/express)

#4 - A new advanced search tool for EMDB (http://pdbe.org/emsearch)

#5 - New visual analysis pages and volume/model viewers for EMDB entries 

#6 - Improved atlas pages for PDB entries

#7 - BioBar made compatible with the latest version of Firefox 

#8 - Many other smaller (or "under-the-hood") improvements


The nitty-gritty details for the eager structure user:

#1 - A new PDB archive browser has been added (see http://pdbe.org/browse for 
an overview of all available browser modules). The new module allows analysis 
of the archive by the GO terms (http://geneontology.org/) assigned to the 
protein(s) in each entry. GO, or Gene Ontology, terms are assigned to UniProt 
(http://uniprot.org/) entries and this annotation is mapped onto relevant 
proteins or protein fragments in PDB entries as part of the SIFTS project 
(http://pdbe.org/sifts). This means that for almost every protein in the PDB, 
there is annotation about its molecular function, cellular component and 
biological process. For example, if you want to find out what structures are 
in the PDB related to programmed cell death, from which species, representing 
which protein families, etc., the GO browser will give you the answer in 
seconds. You can also traverse the GO "graph" interactively and select terms 
above or below "programmed cell death", e.g. "autophagic cell death". You can 
access the new PDB browser module at http://pdbe.org/go

#2 - PDBe have developed a new service to provide information about the status 
of any or all entries (PDB codes) that are, have been, or will be part of the 
archive. You can search in various ways, e.g. by PDB code (if you want to know 
the status of an entry you deposited), by author or keyword (to find out what 
the competition is doing), by method, by period and by status. So, if you want 
to find out how many NMR entries were made obsolete in 2011, or how many 
ribosome structures are on hold until publication, this is the tool for you. 
Try it out at http://pdbe.org/status

#3 - PDBeMotif (http://pdbe.org/motif) is a very powerful tool for analysing 
PDB entries in terms of structure, sequence and chemistry. However, it is also 
quite complex to use. For this reason, we are developing small modules of 
PDBeMotif (and other) functionality that are presented in such a way that they 
are very easy to use by non-experts and provide answers to common but complex 
questions. We have developed a new module to answer the question "Which 
enzymes interact with this ligand?", and we have improved one of the earlier 
modules. Try it out at http://pdbe.org/express

#4 - PDBe have developed a new and flexible search service for the EMDB 
archive. Give it a go at http://pdbe.org/emsearch

#5 - EMDataBank serves summary pages about EMDB entries from RCSB and PDBe. 
Both sites now serve pages with an OpenAstexViewer-based volume and model 
viewer - for example: 
http://www.ebi.ac.uk/emdb-srv/atlas/5119_openastexviewer.html - so you can 
easily see how the fitted model from the PDB fits inside the volume from EMDB. 
PDBe also serves visual map analysis pages - e.g. 
http://www.ebi.ac.uk/emdb-srv/atlas/1564_mapoverview.html - with graphs and 
static images that enable you to assess if the density was masked, if the 
contour level is appropriate, how each of the PDB models fits inside the 
density, etc.

#6 - The atlas pages for many PDB entries have been improved:
   * for entries with ligands for which there is bioactivity data available in 
ChEMBL (https://www.ebi.ac.uk/chembl/), we include a widget on the ligand page 
- try http://pdbe.org/1cbs/ligands - you can click on the graphs and further 
explore the available data in ChEMBL
   * annotation (e.g., InterPro and GO classifications) for chimeric proteins 
has been properly separated for the constituent proteins, e.g. for 
   * for entries containing fragments of proteins, the GO and other annotations 
now pertain only to the fragment that was included in the sample, not the 
entire UniProt sequence
   * if an entry has been released, but the experimental data is still on hold, 
this is shown on the summary page, e.g. for http://pdbe.org/3tuw
   * if the experimental data for an entry has been used by a different set of 
authors to re-refine the structure, a comment and a link is placed on the 
summary page of both entries, e.g. http://pdbe.org/2gwx and 

#7 - Biobar is a bioinformatics-oriented browsing toolbar for Firefox that 
provides access to major biological data resources directly from your browser. 
BioBar has now been made compatible with the latest version of Firefox and a 
couple of bugs have been fixed. For more information and installation of the 
plug-in, surf to http://pdbe.org/biobar

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 warmly 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.


P.S.: In case you had forgotten, last year we released new features such as 
Quips (http://pdbe.org/quips), a "slideshow widget" called PDBportfolio 
(http://pdbe.org/portfolio), a compound-based and a taxonomy-based PDB browser 
(http://pdbe.org/compounds and http://pdbe.org/taxonomy), PDB highlights 
(http://pdbe.org/highlights), a user-friendly overview of every weekly release 
(http://pdbe.org/latest) of both PDB (in terms of both entries and chemical 
compounds) and EMDB (maps and headers), a widget to display coverage of a 
UniProt entry in the PDB (http://pdbe.org/unipdb), easy-to-use analyses of the 
PDB (http://pdbe.org/express), a tool for validation and analysis of NMR 
models in the PDB (http:/pdbe.org/vivaldi), a data-mining tool for EMDB 
(http://pdbe.org/emstats), and revamped NMR (http://pdbe.org/nmr) and 
EM-related pages (http://pdbe.org/emdb).

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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