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News (8)

Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

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

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

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

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

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

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

The article about Omokage search is published online

Related info.:Omokage search / gmfit

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

Sep 22, 2014. New service: Omokage search

New service: Omokage search

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

    FAQ (2)

    Q: How do you make the images for the structure data? What do their colors mean?

    A: Images of EMDB entries are made for EM Navigator, and ones of PDB entries are for Yorodumi. There are several patterns of coloring.

  • See following items for the details.
  • Related info.:Q: How do you make the movies in EM Navigator? / Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.?

    Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.?

    A: We are making them by full-automatic process using Jmol. Their styles are depend on the data type

    • Orientation:
      • Icosahedral assembly: Original orientation.
      • Helical assembly: 6 orientation (+/- of X, Y, Z direction) images are generated in jpeg format. Then, the largest file is chosen. (large JPEG => many dots/colors)
      • Others: by "rotate best" command of Jmol.
      • Ribosomes: by "rotate best" command of Jmol. Only RNA coordinates are used for the orientation.
    • Color:
      • monomer AUs: by N->C (blue->red) rainbow
      • BUs of monomer AUs: by "color molecule" (Jmol's coloring)
      • multimer AUs and thier BUs (including monomer BUs): by "color chain". For this coloring, Jmol uses not a rainbow color but the colors determined by the chain-ID.
    • Problems:
      • BU models are generated by Jmol's system. It works well for the most data, but there are some exception.
      • Checking and fixing processes of the many (>200,000) images are in progress. There are still some wrong images.

    Related info.:Q: How do you make the images for the structure data? What do their colors mean?

    External links:Jmol: an open-source Java viewer for chemical structures in 3D

    Information (7)

    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

    Yorodumi Docs

    Documentation for Yorodumi, EM Navigator, Omokage, etc.

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


      a program for fitting subunits into density map of complex using GMM (Gaussian Mixture Model)

      URL: http://strcomp.protein.osaka-u.ac.jp/gmfit/

      • Developed by Takeshi Kawabata in IPR, Osaka-univ.
      • Used from Omokage search.

      Related info.:Omokage search / Dec 4, 2015. The article about Omokage search is published online / Re-ranking by gmfit

      External links:Pairwise gmfit

      Re-ranking by gmfit

      The similarity ranking by Omokage search can be re-ordered according to correlation coefficient by gmfit, expecting incorporation of the (potential) benefits of two methods with following properties.

      • MethodSpeedPotential accuracy
        Omokage search
        (iDR profile comparison)
        (sub-msec / 1 comparison)
        (1D profile comparison)
        (Gaussian mixture model fitting)
        (sub-sec / 1 comparison)
        (comparison in 3D space)

      Related info.:gmfit / Omokage search

      Changes in new EM Navigator and Yorodumi

      Changes in new versions of EM Navigator and Yorodumi. (Sep. 2016)

      • Changes:
        • New user interface unified in EM Navigator, Yorodumi & Omokage search, supporting mobile devices as well as PCs.
        • New Yorodumi replace the individual data page ("Detail page" of EM Navigator in the legacy system). It is unified browser for EMDB, PDB, and SASBDB entries integrated with EM Navigator and Omokage search.
        • The viewers (structure/movie viewers) appear in pop-up windows. On a PC, multiple viewer windows can be opened. On mobile devices, the viewers support touch operation.
      • New features:
        • Molmil, molecular structure viewer, and SurfView, surface model viewer for EMDB map data, are available to view the 3D structures. Both viewers support mobile device use.
        • Yorodumi support SASBDB entries.
        • Some new pages such as Yorodumi Papers, citation database of structure data entries and Yorodumi Search, cross search by keywords

      Related info.:EM Navigator / Yorodumi / SurfView / Molmil / Movie viewer / EMN Papers / Yorodumi Papers / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi

      Information from PDBMLplus

      PDBMLplus is the XML format file including additional information relating to individual proteins. Currently, PDB files are lacking a detailed description of function, experimental conditions, and the like. And then such information was included to extended XML database, named PDBMLplus.

      Related info.:PDBj / Function and homology information

      External links:PDBMLplus - PDBj helip / About Functional Details page

      Yorodumi annotation

      Annotation by Yorodumi/EM Navigator manager

      Related info.:Q: Who make these documents? Who develop EM Navigator, Yorodumi, Omokage search, etc?

      About Yorodumi Docs

      Yorodumi Docs

      Documentation for Yorodumi, EM Navigator, Omokage, etc.

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