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Kewl new features on the Protein Data Bank in Europe website - 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) announced a substantial make-over of its website last summer, including the
    Message 1 of 1 , Mar 2, 2011
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      Hi all,

      As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org)
      announced a substantial make-over of its website last summer, including the
      release of a number of new features (such as PDBprints -
      http://pdbe.org/pdbprints - and a biologist-friendly structure browser -
      http://pdbe.org/browse). Now we are proud to announce a further update which
      brings several new tools and services as well as lots of improvements "under
      the hood" (performance, presentation, search speed, etc.).

      As always, the URL http://pdbe.org will take you to the PDBe website.

      - One of the first things you'll probably notice is a protein structure on the
      right. This is an appetiser for a new feature called "Quips" ("QUite
      Interesting PDB Structures"). Quips are short stories about one or more
      interesting or topical structures, coupled with an interactive viewer and
      often a tutorial that allows users to delve a bit deeper using one or more
      PDBe resources. Try it out at: http://pdbe.org/quips

      - If you look at the left of the front page, you'll find three new options at
      the top of the PDBe Tools menu - these give you quick access to the latest PDB
      and EMDB entries and (uniquely, we think) to new or revised chemical compounds
      in the PDB. The results are presented in a fresh new way (as opposed to a
      simple table or list) where each entry or ligand comes with annotation, an
      image, and buttons that take you to related pages or that launch PDBe services
      for that particular entry or compound. Give it a go at: http://pdbe.org/latest

      - Speaking of chemical compounds in the PDB, the biologist-friendly structure
      browser (a.k.a. PDBeXplore) now has a new module that allows browsing and
      analysis of all entries that bind a certain chemical compound. Try it out with
      your favourite compound (or try ATP) at: http://pdbe.org/compounds (By the
      way, all the previous browser modules have undergone significant improvements
      and speed-up.)

      - We have begun to incorporate or emulate some of the functionality offered by
      our colleagues at PDBsum. For example, our enzyme browser
      (http://pdbe.org/enzymes) now lists for every EC class you select how many
      structures there are in the PDB for that class. In this release of the website
      we also introduce PDBsum-inspired "PDB highlights", e.g. the oldest entries in
      the current release, the highest resolution crystal structures, the longest
      protein chains, etc. You can find them here: http://pdbe.org/highlights

      - Searches of the PDB and EMDB from the search box in the top bar of the PDBe
      front page have also been improved and the results are now presented in the
      same way as the latest entries and the highlights. You can also type the name
      of a PDBe service (such as pdbefold or pdbepisa) in the search box and the
      system will take you to the appropriate page. The search box is available on
      the front page at http://pdbe.org/ (or if you just want to see a quick
      example, with hits in both PDB and EMDB, try:
      http://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term=baumeister)

      - We introduce a new widget called PDBportfolio that we hope will soon be in
      widespread use on webpages everywhere (for instance:
      http://xray.bmc.uu.se/gerard/structures_pdbportfolio.html). For one or more
      PDB entries, PDBportfolio presents an annotated slideshow consisting of
      informative images, annotation and links for further information or
      exploration. Categories of information covered (in this first release of the
      widget) include the quaternary structure, contents of the deposited entry,
      Pfam/CATH/SCOP domain mappings on the structure, binding environment of one or
      more ligands and experiment-related information. To read more about this
      widget, go to: http://pdbe.org/portfolio PDBportfolio is already in use at the
      Uppsala Electron-Density Server, e.g.:
      http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs

      - Our PDB Atlas pages have also been improved. The summary pages include the
      PDBportfolio widget discussed above (e.g.: http://pdbe.org/1cbs) and you can
      now launch protein-sequence searches of the entire PDB directly from the
      primary structure pages (e.g.: http://pdbe.org/1fss/primary) - simply click on
      the friendly green button labelled "Related PDB sequences". Further, we now
      provide Atlas pages for all possible PDB codes. If an entry is not in the
      current release of the archive, a message will be displayed that informs you
      about its status (e.g., theoretical model, superseded entry, deposited but not
      yet released entry, etc.) An example: http://pdbe.org/2y8d

      - On the front page (under the "About us" tab) we now maintain a list of
      upcoming events in which PDBe staff will participate (roadshows, conferences,
      etc.). If you should participate in an event on this list, come and say hello!
      If you are interested in attending a roadshow from the list, get in touch. A
      shortcut to this page is: http://pdbe.org/events

      - PDBe is now on Facebook. To get the latest PDBe updates in your Facebook
      news feed, simply "like" us -
      http://www.facebook.com/pages/Protein-Data-Bank-in-Europe-PDBe/153011668068957

      - Finally, in January's Database issue of Nucleic Acids Research you can find
      an article describing recent developments and future plans of the Protein Data
      Bank in Europe - you can read or download the paper here:
      http://nar.oxfordjournals.org/content/39/suppl_1/D402

      --Gerard

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