3D electron microscopy data browser

URL: https://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

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 are the data sources of EM Navigator? / Yorodumi Search / Jul 5, 2019. Downlodablable text data

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 are the data sources of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

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.:EM Navigator

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:
• "Resolution" vs. "Method"
• "Specimen temperature" vs. "Resolution"

Related info.:Q: What are the data sources of EM Navigator? / EM Navigator / Mar 30, 2013. New page of EM Navigator, EMN Statistics

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

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

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

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 / Mar 5, 2020. Novel coronavirus structure data

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

Documentation for Yorodumi, EM Navigator, Omokage, etc.

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

Page for Covid-19 featured contents

URL: https://pdbj.org/emnavi/covid19.php

Related info.:Comparison of 3 databanks / Aug 12, 2020. Covid-19 info

Function & Homology similarity search

URL: https://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