Covid-19 info

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

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

• International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
• The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
• In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
• Severe acute respiratory syndrome coronavirus 2 | Severe acute respiratory syndrome coronavirus 2
• SARS-CoV-2 - Yorodumi Search

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

Major update of PDB

• wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
• This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
• In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
• Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Omokage search got faster

• The computation time became ~1/2 compared to the previous version by re-optimization of data accession.
• Enjoy "shape similarity" of biomolecules, more!

Related info.:Omokage search

Presentation PDF file for IPR seminar on Feb 19.

External links:IPR seminar Feb 19th, 2016 / Presentation PDF

The article about Omokage search is published online

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Suzuki Hirofumi, Kawabata Takeshi, and Nakamura Haruki, Bioinformatics. (2015) btv614

Related info.:Omokage search / gmfit

External links:Main text (HTML, Open Access) / Supplementray data (PDF, Open Access)

Omokage search starts to support SASBDB models

• Models data in SASBDB are included in the Omokage search database.
• SASBDB is a databank for small angle scattering data.
• A SASBDB model can be used as a search query.
• The search result may include SASBDB models.

Related info.:Omokage search / SASBDB / Comparison of 3 databanks

New service: Omokage search

• Shape similarity search service, Omokage search has started.
• 形状類似検索「Omokage検索」を開始しました。

Related info.:Omokage search

A: Images of EMDB entries are made for EM Navigator, and ones of PDB entries are for Yorodumi. There are several patterns of coloring.

See following items for the details.

Related info.:Q: How do you make the movies in EM Navigator? / Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.? / Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.?

A: in semi-automatic process with UCSF Chimera

• Method:
• We make been creating the images and movies for structure entries in EM Navigator using UCSF Chimera in semi-automatic process.
• Orientation:
• The structures are manually rotated to be seen in "good" orientation (usually, figures of the paper is refererd), or in similar orientation with similar structure data.
• For the case of icosahedral symmetry structure data, they are viewed normal to their five-fold axis, while typical view of such the structure data are along the two-fold or three-fold axes. This is to unify the orientation with structure data with pseudo-icosahedral symmetry, such as bacteriophage with tail structures.
• Color:
• In EM Navigator, multiple images are made for a single entry. In Omokage search, image of "colored surface view" are shown.
• The surface are colored by height, distance, or cylindrical radius. See the detail page for the coloring of particular images.

Related info.:Q: How do you make the images of PDB entries in Yorodumi, Omokage, etc.? / Q: How do you make the movies in EM Navigator? / Q: How do you make the images for the structure data? What do their colors mean?

External links:UCSF Chimera Home Page

A: We are making them by full-automatic process using Jmol. Their styles are depend on the data type

• Orientation:
• Icosahedral assembly: Original orientation.
• Helical assembly: 6 orientation (+/- of X, Y, Z direction) images are generated in jpeg format. Then, the largest file is chosen. (large JPEG => many dots/colors)
• Others: by "rotate best" command of Jmol.
• Ribosomes: by "rotate best" command of Jmol. Only RNA coordinates are used for the orientation.
• Color:
• monomer AUs: by N->C (blue->red) rainbow
• BUs of monomer AUs: by "color molecule" (Jmol's coloring)
• multimer AUs and thier BUs (including monomer BUs): by "color chain". For this coloring, Jmol uses not a rainbow color but the colors determined by the chain-ID.
• Problems:
• BU models are generated by Jmol's system. It works well for the most data, but there are some exception.
• Checking and fixing processes of the many (>200,000) images are in progress. There are still some wrong images.

Related info.:Q: How do you make the images of EMDB entries in Yorodumi, Omokage, etc.?

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

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

A program for fitting subunits into density map of complex using GMM (Gaussian Mixture Model)

URL: https://pdbj.org/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

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.

Related info.:gmfit / Omokage search

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

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 - PDBJ help

Annotation by Yorodumi/EM Navigator manager

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