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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 7,320 items

Homo sapiens (human)161841637237
Escherichia coli (E. coli)627789148
Mus musculus (house mouse)364620542
Saccharomyces cerevisiae (baker's yeast)73534217
synthetic construct (others)357358627
Bos taurus (cattle)319280321
Rattus norvegicus (Norway rat)174291612
Mycobacterium tuberculosis (bacteria)2418864
Human immunodeficiency virus 122015600
Gallus gallus (chicken)4716459
Thermus thermophilus (bacteria)4314960
Pseudomonas aeruginosa (bacteria)2214411
Staphylococcus aureus (bacteria)21136311
Bacillus subtilis (bacteria)4312951
Arabidopsis thaliana (thale cress)22124717
Escherichia coli K-12 (bacteria)112106419
Oryctolagus cuniculus (rabbit)2328191
Sus scrofa (pig)1518820
Saccharomyces cerevisiae S288C (yeast)15679918
Drosophila melanogaster (fruit fly)488957


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