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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

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Oct 5, 2021. Nobel Prize for mechanically activated and temperature-gated ion channels

Nobel Prize for mechanically activated and temperature-gated ion channels

  • The Nobel Prize in Physiology or Medicine 2021 was awarded jointly to David Julius and Ardem Patapoutian "for their discoveries of receptors for temperature and touch."
  • EM Navigator can help to find cryo-EM structure data by both pioneers.

External links:The Nobel Prize in Physiology or Medicine 2021 - NobelPrize.org / Structure data by Ardem Patapoutian / Structure data by David Julius

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Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

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Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

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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.

PageDataFormat
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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 file for IPR seminar on Feb 19.

Presentation PDF file for IPR seminar on Feb 19.

External links:IPR seminar Feb 19th, 2016 / Presentation PDF

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

The article about Omokage search is published online

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Suzuki Hirofumi, Kawabata Takeshi, and Nakamura Haruki, Bioinformatics. (2015) btv614

Related info.:Omokage search / gmfit

External links:Main text (HTML, Open Access) / Supplementray data (PDF, Open Access)

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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 included in 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. Multiple "PDB "SPLIT" entries are replaced with single "LARGE" entries

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

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

External links:Integration of Large Structures with the Main PDB Archive

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Sep 22, 2014. New service: Omokage search

New service: Omokage search

  • Shape similarity search service, Omokage search has started.
  • 形状類似検索「Omokage検索」を開始しました。

Related info.:Omokage search

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Mar 30, 2013. New page of EM Navigator, EMN Statistics

New page of EM Navigator, EMN Statistics

EMN 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.
  • 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".

External links:Announcement: EMDB header format update

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