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More cool stuff from the Protein Data Bank in Europe (pdbe.org)

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  • Gerard DVD Kleywegt
    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
    Message 1 of 1 , Jul 6, 2011
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      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
      headers).

      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.
      http://pdbe.org/unipdb?uniprot=P03023

      #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
      (http://pdbe.org/emstats)

      #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
      http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Structural_motifs_in_the_PDB).
      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
      http://pdbe.org/vivaldi/2keo

      - 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 http://pdbe.org/emstats

      - 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
      http://pdbe.org/?tab=resources&subtab=ftpaccess
      * 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
      (http://pdbe.org/fold).
      * 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:
      http://pdbe.org/latest

      - 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:
      http://scripts.iucr.org/cgi-bin/paper?S090744491004117X

      ------------------

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

      --Gerard

      ---
      Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
      gerard@... ..................... pdbe.org
      Secretary: Pauline Haslam pdbe_admin@...

      ------------------

      Footnotes:

      [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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