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News (14)

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Feb 20, 2018. PDBj/BINDS workshop in Osaka University

PDBj/BINDS workshop in Osaka University

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    Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

    Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

    • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
    • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
    • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

    External links: The 2017 Nobel Prize in Chemistry - Press Release

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    Jul 12, 2017. Major update of PDB

    Major update of PDB

    • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
    • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

    External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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    Jun 16, 2017. Omokage search with filter

    Omokage search with filter

    • Result of Omokage search can be filtered by keywords and the database types

    Related info.: Omokage search

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    Sep 15, 2016. EM Navigator & Yorodumi renewed

    EM Navigator & Yorodumi renewed

    • New versions of EM Navigator and Yorodumi started

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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    Aug 31, 2016. New EM Navigator & Yorodumi

    New EM Navigator & Yorodumi

    • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
    • Current version will continue as 'legacy version' for some time.

    Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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    Apr 13, 2016. Omokage search got faster

    Omokage search got faster

    • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
    • Enjoy "shape similarity" of biomolecules, more!

    Related info.: Omokage search

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    Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

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    Dec 4, 2015. The article about Omokage search is published online

    The article about Omokage search is published online

    Related info.: Omokage search / gmfit

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    Nov 28, 2015. Omokage search starts to support SASBDB models

    Omokage search starts to support SASBDB models

    • Models data in SASBDB are added to the Omokage search database.
    • SASBDB is a databank for small angle scattering data
    • A SASBDB model can be used as a search query.
    • The search result may include SASBDB models.

    Related info.: Omokage search / SASBDB / Comparison of 3 databanks

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    Dec 10, 2014. PDB "SPLIT" entries are replaced with "LARGE" entries

    PDB "SPLIT" entries are replaced with "LARGE" entries

    • Structure data deposited as multiple PDB entries are replace with single combined entries, which were previously stored as "large structure". See here for details.
    • In EM Navigator, many ribosome and several virus entries are replaced.

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    Sep 22, 2014. New service: Omokage search

    New service: Omokage search

  • Shape similarity search service, Omokage search has started.
  • Related info.: Omokage search

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    Mar 30, 2013. New page of in EM Navigator, statistics

    New page of in EM Navigator, statistics

    Related info.: EMN Statistics

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    Jan 16, 2013. New EMDB header format

    New EMDB header format

    • Format of the EMDB header file (XML based meta data file, not the map data themselves) are updated to version 1.9 (see here for details)
    • Now, the contents of EM Navigator are based on the new data. Colors of some parts (e.g. bars in top area of the Detail pages) indicate 3D-reconstruction method, instead of 'aggregation states'.

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