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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 7,237 items

Homo sapiens (human)149740954225
Escherichia coli (E. coli)615786248
Mus musculus (house mouse)324614642
Saccharomyces cerevisiae (baker's yeast)70334147
synthetic construct (others)333346627
Bos taurus (cattle)313278921
Rattus norvegicus (Norway rat)16529088
Mycobacterium tuberculosis (bacteria)2018814
Human immunodeficiency virus 121015300
Gallus gallus (chicken)4616269
Thermus thermophilus (bacteria)4314960
Pseudomonas aeruginosa (bacteria)2214281
Staphylococcus aureus (bacteria)20135911
Bacillus subtilis (bacteria)4312891
Arabidopsis thaliana (thale cress)19123217
Escherichia coli K-12 (bacteria)109103119
Sus scrofa (pig)1458750
Oryctolagus cuniculus (rabbit)1958041
Escherichia virus T4 (bacteriophage)349040
Drosophila melanogaster (fruit fly)478837


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