-Search & filter documents
3D electron microscopy data browser
- 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
3DEM data search
- 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
Database of articles cited by 3DEM data entries
- 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
Image gallery of 3DEM data
- Categorization is done by EM Navigator manager manually. It is not strict.
Related info.: EMDB / PDB / EM Navigator
Statistics of 3DEM data in table and graph styles
- 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.
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
Thousand views of thousand structures
- 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
Cross-search of EMDB, PDB, SASBDB, etc.
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
Database of articles cited by EMDB/PDB/SASBDB data
- 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
Taxonomy data in EMDB/PDB/SASBDB
- Taxonomy database of sample sources of data in EMDB/PDB/SASBDB
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks
Search structure by SHAPE
- "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
Documentation for Yorodumi, EM Navigator, Omokage, etc.
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
An open-source viewer for chemical structures in 3D
|X-Y rotation||X-Y move||Zoom in/out|
|Mouse||left drag||[Ctrl] + right drag||center drag (vertical) / wheel|
|Touch||single finger||double finger||pinch|
Related info.: Molmil / Yorodumi
External links: Jmol: an open-source Java viewer for chemical structures in 3D
WebGL based molecular viewer
- Mouse/touch operation
X-Y rotation X-Y move Zoom in/out Mouse left drag center drag / shift + left drag right drag / wheel Function menu: top left buttons on viewer screen Touch single finger pinch
Related info.: Jmol/JSmol / SurfView / Changes in new EM Navigator and Yorodumi
EMDB map surface models viewer on Web browsers
- 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 rotation X-Y move Zoom in/out Mouse left drag right drag center drag / wheel Touch single finger double finger pinch
Related info.: Movie viewer / Molmil / Changes in new EM Navigator and Yorodumi
+Comparison of 3 databanks
|method||various||3DEM||SAS (Small Angle Scattering)|
|main data||atomic model||3D map||SAS profile (+/- 3D models)|
|str. data format||PDBx/mmCIF, etc.||CCP4 map||PDB + sasCIF|
|meta data format||PDBx/mmCIF, etc.||EMDB XML||ASCII + sasCIF|
Related info.: EMDB / PDB / SASBDB / Omokage search / Experimental methods, equipments, and software data
Electron Microscopy Data Bank, Databank for 3DEM
Related info.: 3D electron microscopy (3DEM) / Comparison of 3 databanks
Protein Data Bank - The single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.
Related info.: PDBj / Comparison of 3 databanks
External links: World Wide PDB
Protein Data Bank Japan.
Related info.: PDB / Information from PDBMLplus
Small Angle Scattering Biological Data Bank - Curated repository for small angle scattering data and models
- Develop & manage: BioSAXS group in EMBL
- Since 2014
Related info.: Comparison of 3 databanks
a program for fitting subunits into density map of complex using GMM (Gaussian Mixture Model)
- 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
+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 states Methods 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)
+electron cryo microscopy (cryoEM)
Electron microscopy where the sample is studied at cryogenic temperatures
Related info.: 3D electron microscopy (3DEM) / Q: Is 3DEM same as electron cryo microscopy (cryoEM)?
External links: Cryo-electron microscopy - Wikipedia
+"Movies out of date"
Movies with this annotation may not be up-to-date.
Related info.: Q: How do you make the movies in EM Navigator?
+Experimental methods, equipments, and software data
Database of experimental methods of EMDB, PDB and SABDB.
Related info.: Comparison of 3 databanks / Yorodumi Search
+Function and homology information
Molecular function, domain, and homology information from related databases.
Related info.: Information from PDBMLplus / Yorodumi Search / Yorodumi
+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.
Method Speed Potential 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)
- 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
Annotation by Yorodumi/EM Navigator manager
Related info.: Q: Who make these documents? Who develop EM Navigator, Yorodumi, Omokage search, etc?
-About Yorodumi Docs
Documentation for Yorodumi, EM Navigator, Omokage, etc.