-Search & filter documents
FAQ, News, Information, EM Navigator, Yorodumi, Omokage search, Services, All docs
-Information (13)
+EM Navigator
3D electron microscopy data browser
URL: https://pdbjlvh1.pdbj.org/emnavi/.
- EM Navigator is a browser for 3D electron microscopy (3D-EM) data of biological molecules and assemblies.
- It provides EMDB-PDB cross-search, statistical information, and links to similar structures.
- You can easily check the latest EM structural data and structural papers.
Related info.:EMDB / PDB / PDBj / Q: What are the data sources of EM Navigator? / EMN Search / EMN Papers / EMN Gallery / EMN Statistics / Changes in new EM Navigator and Yorodumi
+EMN Search
3DEM data search
URL: https://pdbjlvh1.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 are the data sources of EM Navigator? / Yorodumi Search / Jul 5, 2019. Downlodablable text data
+EMN Papers
Database of articles cited by 3DEM data entries
URL: https://pdbjlvh1.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 are the data sources of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi
+EMN Gallery
Image gallery of 3DEM data
URL: https://pdbjlvh1.pdbj.org/emnavi/gallery.php
Categorization is done by EM Navigator manager manually. It is not strict.
Related info.:EM Navigator
+EMN Statistics
Statistics of 3DEM data in table and graph styles
URL: https://pdbjlvh1.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.:Q: What are the data sources of EM Navigator? / EM Navigator / Mar 30, 2013. New page of EM Navigator, EMN Statistics
+Yorodumi
Thousand views of thousand structures
URL: https://pdbjlvh1.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
+Yorodumi Search
Cross-search of EMDB, PDB, SASBDB, etc.
URL: https://pdbjlvh1.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
+Yorodumi Papers
Database of articles cited by EMDB/PDB/SASBDB data
URL: https://pdbjlvh1.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
+Yorodumi Speices
Taxonomy data in EMDB/PDB/SASBDB
URL: https://pdbjlvh1.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 / Mar 5, 2020. Novel coronavirus structure data
+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
+Covid-19 info
Page for Covid-19 featured contents
URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php
Related info.:Comparison of 3 databanks / Aug 12, 2020. Covid-19 info
+F&H Search
Function & Homology similarity search
URL: https://pdbjlvh1.pdbj.org/emnavi/fh-search.php
Based on the similarity of Function & Homolog items related to the structure data, similar data are searched from structure databases.
Related info.:Function and homology information