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Yorodumi Species
- Taxonomy data in EMDB/PDB/SASBDB -

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Name, Taxonomy-ID, or Keywords:

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Showing 1 - 20 of 7,149 items

Homo sapiens (human)137139988183
Escherichia coli (E. coli)600781748
Mus musculus (house mouse)310608842
Saccharomyces cerevisiae (baker's yeast)67334047
synthetic construct (others)311329827
Bos taurus (cattle)288277021
Rattus norvegicus (Norway rat)15028778
Mycobacterium tuberculosis (bacteria)2018584
Human immunodeficiency virus 119715030
Gallus gallus (chicken)4215996
Thermus thermophilus (bacteria)4214960
Pseudomonas aeruginosa (bacteria)2014111
Staphylococcus aureus (bacteria)20133511
Bacillus subtilis (bacteria)4312831
Arabidopsis thaliana (thale cress)13119217
Escherichia coli K-12 (bacteria)10697415
Oryctolagus cuniculus (rabbit)1897921
Sus scrofa (pig)1018680
Escherichia virus T4 (bacteriophage)339020
Drosophila melanogaster (fruit fly)468707


About Yorodumi Species


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. See below links for details.
  • 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

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

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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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Yorodumi Speices

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

Read more