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

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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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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Related docs

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EMDB

Electron Microscopy Data Bank, Databank for 3DEM

URL: https://www.ebi.ac.uk/emdb/

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

External links:The Electron Microscopy Data Bank - EBI / EMDataResource

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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: https://wwPDB.org/

Related info.:PDBj / EMDB

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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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Comparison of 3 databanks

Yorodumi and Omokage can cross-search these DBs

MethodMain dataStr. data formatmeta data format
PDBvariousatomic modelPDBx/mmCIF, etc.PDBx/mmCIF, etc.
EMDB3DEM3D mapCCP4 mapEMDB XML
SASBDBSmall Angle Scattering (SAS)SAS profile
(+/- 3D models)		PDB + sasCIFASCII + sasCIF

Related info.:EMDB / PDB / SASBDB / Covid-19 info / ID/Accession-code notation in Yorodumi/EM Navigator / Experimental methods, equipments, and software data

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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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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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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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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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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.
    CategoryName of database or definition
    Function%Gene ontology, Enzyme Commission number, Reactome, etc.
    Domain/homologyCATH, InterPro, SMART, etc.
    ComponentUniProt, GenBank, PDB chemical component, etc.

Related info.:F&H Search / Information from PDBMLplus / Yorodumi Search / Yorodumi / F&H 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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About Yorodumi Docs

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Yorodumi Docs

Documentation for Yorodumi, EM Navigator, Omokage, etc.

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