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Jul 5, 2019. Downlodablable text data

Downlodablable text data

  • Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.
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    EMN Searchsearch resultCSV, TSV, or JSON
    EMN statisticsdata tableCSV or TSV

Related info.: EMN Search / EMN Statistics

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

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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

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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

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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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