[Protein-crystallography] More cool stuff from the Protein Data Bank in Europe (pdbe.org)

Gerard DVD Kleywegt via xtal-log%40net.bio.net (by gerard from xray.bmc.uu.se)
Wed Jul 6 14:15:24 EST 2011

Hi all,

As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org) 
carried out a substantial make-over of its website last summer, including the 
launch of several new features (such as PDBprints - http://pdbe.org/pdbprints - 
and a biologist-friendly structure browser - http://pdbe.org/browse). Earlier 
this year, there was a further update which included new features such as Quips 
(http://pdbe.org/quips), a "slideshow widget" called PDBportfolio 
(http://pdbe.org/portfolio), a compound-based PDB browser 
(http://pdbe.org/compounds), PDB highlights (http://pdbe.org/highlights) and 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 

Now it's time for the 2011 summer update. Below is a brief description of the 
new features and services - in the coming weeks we will post more detailed 
descriptions of some of these. As always, the URL http://pdbe.org will take you 
to the PDBe website. Most 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.


If you can't wait to find out what cool new features are now available, here 
are the highlights:

#1 - UniPDB (http://pdbe.org/unipdb), a widget for graphical display of 
coverage in the PDB of any UniProt entry, e.g. 

#2 - PDBeXpress (http://pdbe.org/express), several easy-to-use yet powerful 
analyses of the PDB

#3 - taxonomy-based browser of the PDB archive (http://pdbe.org/taxonomy)

#4 - revamped NMR pages (http://pdbe.org/nmr)

#5 - Vivaldi (http:/pdbe.org/vivaldi), interactive visualisation, validation 
and analysis of NMR models and data, e.g. http://pdbe.org/vivaldi/2keo

#6 - revamped EM-related pages (http://pdbe.org/emdb)

#7 - graphs and statistics about contents and trends in the contents of EMDB 

#8 - LeView (http://pdbe.org/leview), a Java tool to create 2D diagrams of 
ligands and the interactions in their binding site

#9 - improved atlas pages for PDB entries, e.g. http://pdbe.org/1cbs

#10 - many other smaller (or "under-the-hood") improvements


A bit more detail:

- UniPDB is a new service that provides instant, graphical, up-to-date 
information (taken from SIFTS; see http://pdbe.org/sifts) about the coverage in 
the PDB of any protein sequence in UniProt. It can be used through the PDBe 
website or be included in your own web pages. For a description, see 
http://pdbe.org/unipdb - for an example, see 
http://pdbe.org/unipdb?uniprot=P03023 (this is for the lac repressor - note how 
the PDBlogos instantly reveal which are X-ray or NMR entries, which entries 
contain DNA, etc.).

- PDBeMotif (http://pdbe.org/motif) is one of the most powerful services 
available for analysing PDB entries in terms of structure, sequence and 
chemistry (for an example, see 
However, it is also quite complex to use. For this reason, we have begun to 
develop 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 (such as: "what ligands can bind in a site that 
contains Arg, Tyr and Asp?" [1] or: "which residue types are found most often 
in the binding sites of retinoic acid?" [2]). From the results pages you can 
explore the hits using the advanced options of PDBeMotif. This service is 
called PDBeXpress and the first modules can be accessed at 
http://pdbe.org/express - we welcome your suggestions for future modules!

- A new PDB browser has been added (see http://pdbe.org/browse for an overview 
of all available browser modules) - it allows analysis of the archive in terms 
of taxonomy. So, if you want to know what the predominant fold class [3] or 
quaternary structure [4] is for all mammalian proteins in the PDB, or who has 
determined the most structures of proteins from P. falciparum [5], this browser 
is for you. You can access it at http://pdbe.org/taxonomy

- The NMR-related pages at PDBe (http://pdbe.org/nmr) have been reorganised. In 
addition, a new service (called Vivaldi) for interactive analysis, display and 
validation of NMR entries in the PDB is now available. It can be used by 
experts and non-experts alike, has a wizard option to help you customise the 
display and provides extensive explanations of the quantities that you are 
displaying (as linear graphs or on the 3D structure). You can can view 
clustering and domain organisation from OLDERADO, analyse validation data from 
CING and VASCO, find out which residues have restraint violations, etc. Well 
worth a try, even (or rather: especially!) if you are not an NMRtist! It can be 
accessed at http:/pdbe.org/vivaldi - for an example, try 

- The Electron Microscopy-related pages at PDBe (http://pdbe.org/emdb) have 
been reorganised. A new service provides up-to-date and interactive graphs and 
statistics about the contents and trends of EMDB. Very useful if you are 
writing an EM-related grant, or are just curious about the development of the 
3DEM field as reflected in the contents of EMDB. You can access this service at 

- LeView (Ligand Environment Viewer) is a new interactive Java tool that can be 
used to create 2D diagrams of ligands and the interactions in their binding 
site. It is not unlike LigPlot, except that it is interactive and customisable. 
The diagrams can be saved in a variety of raster and vector graphics formats. 
Try it out at http://pdbe.org/leview (note: this is a beta release, so we are 
grateful for both bug reports and feature requests)

- The atlas pages for PDB entries have been improved:
   * near the top of a summary page, you will now find several "action buttons" 
that allow you to download the PDB file, view the structure in 3D, launch 
PDBeFold (SSM) to find similar structures in the PDB and access the PDBePISA 
results. For an example, see http://pdbe.org/1cbs
   * summary pages for PDB entries now contain a table listing all UniProt 
entries occurring in the entry, plus buttons that will launch either a sequence 
search of the entire PDB or the UniPDB widget described above. For an example, 
see: http://pdbe.org/1fss
   * ligand pages for PDB entries now contain links to the ChEMBL (bioactivity 
data) and ChEBI (chemical annotation) resources at the EBI. For an example, 
see: http://pdbe.org/1o8v/ligands

- In addition to these new features and services, there have been many other 
changes and additions, including:
   * Highlights can now be listed separately for X-ray, NMR and EM entries in 
the PDB. So if you want to know what the oldest surviving EM entry in the PDB 
is [6], or which NMR entry contains the longest protein chain [7], have a look 
at http://pdbe.org/highlights
   * URL shortcuts have been implemented to give quick access to EMDB entries - 
these are of the form: http://pdbe.org/emd-1180 (the 4-digit number is the EMDB 
code of the entry).
   * We have collected links to all relevant RSS feeds concerning PDBe, wwPDB, 
EMDB and EBI on one page - http://pdbe.org/rss
   * Similarly, available ftp resources at PDBe are now listed at 
   * Many programs and services have been updated or improved "under the hood", 
including the PDBe Wizard (http://pdbe.org/wizard), PDBeMotif 
(http://pdbe.org/motif), PDBePISA (http://pdbe.org/pisa) and PDBeFold 
   * The list of the weekly updates of PDB entries and compounds and EMDB maps 
and headers has been improved. For example, for newly released PDB entries the 
ligands and other non-standard compounds are now listed (hover over their 
three-letter codes with your mouse to see their chemical structures). See: 

- Finally, we maintain an up-to-date list of publications (co-)authored by PDBe 
staff (at http://pdbe.org/publications). If you would like to read about the 
long-term plans of PDBe, our paper in this year's CCP4 Proceedings issue of 
Acta Cryst. D 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.


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



[1] top 5: FAD, NADP, glycerol, NAD and pyridoxal phosphate
[2] top 8: Ala, Leu, Phe, Ile, Val, Arg, Cys, Gln
[3] 40.2% alpha/beta, 35.3% beta, 22.9% alpha
[4] 43.5% monomers, 32.2% heteromultimers, 24.2% homomultimers
[5] top 5: R. Hui (51 entries), SGC (47), Al Edwards (40), Cheryl Arrowsmith 
(40), Johan Weigelt (38)
[6] entry 1brd (http://pdbe.org/1brd), deposited on my mum's birthday in 1990
[7] entry 2vda (http://pdbe.org/2vda), with 828 (!) residues

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