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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.
  • 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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      Movie viewer

      Visualization of 3DEM structure data by movies.

      • Horizontal- and vertical- rotation motions and "slicing" motion are recorded in the movies.
      • As the movie frame can be controlled by mouse/touch position, it can be operated interactively as a molecular viewer. According to the mouse/finger position and orientation of the motion on the movie panel, the model rotates on horizontal or vertical direction. By horizontal mouse/finger movement on the top part of the movie, the slicing motion is shown.

      Related info.: Q: How do you make the movies in EM Navigator? / Q: Can I use the movies and their snapshots in the EM Navigator for papers or presentations? / SurfView / Changes in new EM Navigator and Yorodumi

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      Jmol/JSmol

      An open-source viewer for chemical structures in 3D

    • Mouse/touch operation
      X-Y rotationX-Y moveZoom in/out
      Mouseleft drag[Ctrl] + right dragcenter drag (vertical) / wheel
      Touchsingle fingerdouble fingerpinch
      Jmol menu: [Ctrl] + click / right click
    • Related info.: Molmil / Yorodumi

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

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      Molmil

      WebGL based molecular viewer

      • Molmil runs on Web browser on a smartphone or tablet device as well as PC. (Molmil is based on WebGL and Javascript).
      • Mouse/touch operation
        X-Y rotationX-Y moveZoom in/out
        Mouseleft dragcenter drag / shift + left dragright drag / wheelFunction menu: top left buttons on viewer screen
        Touchsingle fingerpinch

      Related info.: Jmol/JSmol / SurfView / Changes in new EM Navigator and Yorodumi

      External links: Documentation of Molmil in PDBj site / Molmil's page in GitHub

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      SurfView

      EMDB map surface models viewer on Web browsers

      • SurfView run on Web browser on a smartphone or tablet device as well as PC. (SurfView is based on a WebGL and three.js, Javascript 3D library)
      • The surface models shwon in this viewer are modified for simplification and data size reduction. To get views of full-resolution data, see movies instead.
      • Mouse/touch operation
        X-Y rotationX-Y moveZoom in/out
        Mouseleft dragright dragcenter drag / wheel
        Touchsingle fingerdouble fingerpinch

      Related info.: Movie viewer / Molmil / Changes in new EM Navigator and Yorodumi

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      Comparison of 3 databanks

    • Yorodumi and Omokage can cross-search these DBs.
      PDBEMDBSASBDB
      methodvarious3DEMSAS (Small Angle Scattering)
      main dataatomic model3D mapSAS profile (+/- 3D models)
      str. data formatPDBx/mmCIF, etc.CCP4 mapPDB + sasCIF
      meta data formatPDBx/mmCIF, etc.EMDB XMLASCII + sasCIF
    • Related info.: EMDB / PDB / SASBDB / Omokage search / Experimental methods, equipments, and software data

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      EMDB

      Electron Microscopy Data Bank, Databank for 3DEM

      URL: http://emdatabank.org/

      Related info.: 3D electron microscopy (3DEM) / Comparison of 3 databanks

      External links: EMDataBank.org / The Electron Microscopy Data Bank (PDBe site) / EM Data Bank - Wikipedia

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      PDB

      Protein Data Bank - The single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

      URL: http://wwPDB.org/

      Related info.: PDBj / Comparison of 3 databanks

      External links: World Wide PDB

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      PDBj

      Protein Data Bank Japan.

      URL: http://pdbj.org/

    • A member of wwPDB.
    • Related info.: PDB / Information from PDBMLplus

      External links: PDBj@Facebook / PDBj@Twitter / Haruki Nakamura Lab., Institute of Protein Research,Osaka University

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      SASBDB

      Small Angle Scattering Biological Data Bank - Curated repository for small angle scattering data and models

      URL: http://www.sasbdb.org/

      • Develop & manage: BioSAXS group in EMBL
      • Since 2014

      Related info.: Comparison of 3 databanks

      External links: Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI. SASBDB, a repository for biological small-angle scattering data. Nucleic Acids Res. 2015 Jan 28;43:D357-63.

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      gmfit

      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

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      3D electron microscopy (3DEM)

      A generic term of electron microscopic analyses to obtain 3D structures

      • Analyses such as electron tomography, single particle analysis, and electron diffraction are included.
        Aggregation statesMethods generally used
        "individual structure"electron tomography
        "single particle"single particle analysis
        "icosahedral"single particle analysis
        "helical"helical reconstruction / single particle analysis
        "2D-crystal"electron diffraction / Fourier filtering
      • Characteristics compared to X-ray crystallography and NMR:
        • Advantage: Wider applicability of sample (not require high-purity or high-concentration smaple, and useful for more huge, complex, flexible, and less uniform sample)
        • Disadvantage: Lower resolution (hard to get atomic-level resolution data)

      Related info.: EMDB / electron cryo microscopy (cryoEM)

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      electron cryo microscopy (cryoEM)

      Electron microscopy where the sample is studied at cryogenic temperatures

    • The specimen is cooled at 4~100K (-269~-170℃) to keep it in hydrated state in the highly vaqumed environment, and to reduce radiation dammage by electron beam.
    • Related info.: 3D electron microscopy (3DEM) / Q: Is 3DEM same as electron cryo microscopy (cryoEM)?

      External links: Cryo-electron microscopy - Wikipedia

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      "Movies out of date"

      Movies with this annotation may not be up-to-date.

    • EMDB map data are sometimes remediated. Unfortunately, the process of making movies in the EM Navigaotr are not fully automated, and it is very hard to remake the all to catch up. So, some movies and movie parameters are based on the older data, and may be improper for new map data.
    • Related info.: Q: How do you make the movies in EM Navigator?

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      Experimental methods, equipments, and software data

      Database of experimental methods of EMDB, PDB and SABDB.

      Related info.: Comparison of 3 databanks / Yorodumi Search

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      Function and homology information

      Molecular function, domain, and homology information from related databases.

    • To help to understand the molecular function and to find the related structure data, Yorodumi and Yorodumi Search display and utilize the related database information about function and homology. In addition to the information of EC, EMBL, GeneBank, GO, InterPro, UniProt, etc. stored in the EMDB header XML, PDBx/mmCIF and sasCIF original data, information of Pfam, PROSITE, Reactome, UniProkKB, etc. are collected via PDBMLplus, EMDB-PDB fitting data, and/or UniProt.
    • Related info.: Information from PDBMLplus / Yorodumi Search / Yorodumi

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      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)
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        (sub-msec / 1 comparison)
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        (1D profile comparison)
        gmfit
        (Gaussian mixture model fitting)
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        (sub-sec / 1 comparison)
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        (comparison in 3D space)

      Related info.: gmfit / Omokage search

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      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

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      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

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      Yorodumi annotation

      Annotation by Yorodumi/EM Navigator manager

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

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      About Yorodumi Docs

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      Yorodumi Docs

      Documentation for Yorodumi, EM Navigator, Omokage, etc.

        Read more