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- Documentation for Yorodumi, EM Navigator, Omokage, etc. -

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Information (11)

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EM Navigator

3D electron microscopy data browser

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

  • Browser for 3D electron microscopy (3D-EM) data of biological molecules and assemblies.

Related info.: EMDB / PDB / PDBj / Q: What is the data source of EM Navigator? / EMN Search / EMN Papers / EMN Gallery / EMN Statistics / Changes in new EM Navigator and Yorodumi

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EMN Search

3DEM data search

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

  • Advanced data search for EMDB and EM data in PDB widh various search and display options

Related info.: EMDB / PDB / EM Navigator / Q: What is the data source of EM Navigator? / Yorodumi Search

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EMN Papers

Database of articles cited by 3DEM data entries

URL: https://pdbj.org/emnavi/pap.php?em=1

  • Database of articles cited by 3DEM data entries in EMDB and PDB
  • Using PubMed data

Related info.: EMDB / PDB / Q: What is the data source of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

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EMN Gallery

Image gallery of 3DEM data

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

  • Categorization is done by EM Navigator manager manually. It is not strict.

Related info.: EMDB / PDB / EM Navigator

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EMN Statistics

Statistics of 3DEM data in table and graph styles

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

  • The table can be sorted. Click the column header to be sorted. (second click to reverse, [Shift]+click for multi-column sort)
  • To show the bar graph in table mode, point the column/row header by mouse courser.
  • To search the correspoinding data, click the cell of value.
  • Examples:

Related info.: EMDB / PDB / Q: What is the data source of EM Navigator? / EM Navigator / Mar 30, 2013. New page of in EM Navigator, statistics

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Yorodumi

Thousand views of thousand structures

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

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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Yorodumi Search

Cross-search of EMDB, PDB, SASBDB, etc.

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

    Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / EMN Search / Yorodumi / Experimental methods, equipments, and software data / Function and homology information / Changes in new EM Navigator and Yorodumi

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    Yorodumi Papers

    Database of articles cited by EMDB/PDB/SASBDB data

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

    • Database of articles cited by EMDB, PDB, and SASBDB entries
    • Using PubMed data

    Related info.: EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

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    Yorodumi Speices

    Taxonomy data in EMDB/PDB/SASBDB

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

    • Taxonomy database of sample sources of data in EMDB/PDB/SASBDB

    Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks

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    Omokage search

    Search structure by SHAPE

    URL: https://pdbj.org/omokage/

    • "Omokage search" is a shape similarity search service for 3D structures of macromolecules. By comparing global shapes, and ignoring details, similar-shaped structures are searched.
    • The search is performed ageinst >200,000 structure data, which consists of EMDB map data, PDB coordinates (deposited units (asymmetric units, usually), PDB biological units, and SASBDB mdoels).
    • For the search query, you can use either a data in the PDB/EMDB/SASBDB or your original model.
    • Supported formats are PDB (atomic model, SAXS bead model, etc.) and CCP4/MRC map (3D density map).
    • Shape comparison is performed by iDR profile method, which uses 1D-distance profiles of super-simplified models generated by vector quantizaion in Situs package.

    Related info.: Comparison of 3 databanks / Sep 22, 2014. New service: Omokage search / gmfit / Re-ranking by gmfit

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    Yorodumi Docs

    Documentation for Yorodumi, EM Navigator, Omokage, etc.

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

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      About Yorodumi Docs

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      Yorodumi Docs

      Documentation for Yorodumi, EM Navigator, Omokage, etc.

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