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Omokage search
- Shape similarity search of macromolecules -

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Search query

Query structure data:

ID of EMDB, PDB or SASBDB:
  • EMDB map
    • 4 or 5 digit ID
    • or string starts with "e"
    • e.g. 1003, EMD-1003, e1003
  • PDB deposited unit (asymetric unit, AU)
    • 4 letter ID code
    • or ID code + hyphen + "d"
    • e.g. 100d, 100d-d
  • PDB assembly (biological unit, BU)
    • ID + hyphen + assembly-ID
    • Or click the image of AU/BU, which will be shown below when you input an PDB-ID
    • e.g. 1oel-1
  • SASBDB model
    • SASBDB-ID
    • or SASBDB-model-ID
    • e.g. SASDAA5, 100, sas-100
Comparison of 3 databanks

Samples:

Structure data giving symbolic results

This is an EM map data of the RNA polymerase II at 25 A resolution. You will find atomic models and EM maps of RNA polymerase structures from the EMDB & PDB._Perform search.

The DNA clamp is a ring shaped oligomer essential for DNA metabolism. All the DNA clamps have similar shapes, while bacterial clamps are dimer ring, and archaeal/eukaryal ones are trimer ring. By search using this trimer clamp, you will find dimer clamp structures as well._Perform search.

EF-Tu/tRNA complex (RNA + protein) and EF-G (monomeric protein) have similar shapes despite their different compositions ("molecular mimicry"). You will find both EFs by this search._Perform search.

This is a dummy-atom model of lumazine synthase obtained by SAS. You will find many crystal structures and EM maps of same molecules._Perform search.

Many 70S ribosome structure data are stored in EMDB and PDB. Omokage search is useful to find out such the huge molecule structures._Perform search.

For huger molecule, such as this rice dwarf virus, Omokage search can be used._Perform search.

Not only for the huge structures but also for small molecules, such as this DNA fragment, this tool might be useful. By this search, some proteins having similar shape to this DNA fragment are found (for good or for bad)._Perform search.

This is another example for small molecules. Which proteins have simialar shapes to this beta-propeller structure?_Perform search.

EMDB

PDB

SASBDB

You can use your original data or a modified data for the search. Select type of the file and upload the file by this form.

Data type:

  • This is a search using PDB format coordinate file (atomic model, SAXS bead model, etc)
  • Uncompressed or gzip-compressed file can be used
File
  • This is a search using 3D density map file in CCP4/MRC format.
  • Only for map with cubic voxels.
  • Max voxel number is ~200. Large map data should be trimmed and shrined before uploading.
  • Uncompressed or gzip-compressed file can be used
File
Surface level
  • This is a search using "Codebook" vectors made by qvol or qpdb tool in Situs package. Two models, model with 30 and 50 points are required for Omokage comparison. " ,
30-dot model
50-dot model

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Identical assembly

Assembly #1 of PDB-1n4l is identical to the deposited model. Search is performed using deposited model.

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About Omokage search

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News

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Aug 12, 2020. Covid-19 info

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

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Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

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

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

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Jul 12, 2017. Major update of PDB

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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

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

Related info.:Omokage search

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Apr 13, 2016. Omokage search got faster

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

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Omokage search

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

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