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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 7,415 items

Homo sapiens (human)175342254247
Escherichia coli (E. coli)640791748
Mus musculus (house mouse)387626642
Saccharomyces cerevisiae (baker's yeast)82334417
synthetic construct (others)407368927
Bos taurus (cattle)345282220
Rattus norvegicus (Norway rat)201295712
Mycobacterium tuberculosis (bacteria)2818934
Human immunodeficiency virus 123315900
Gallus gallus (chicken)4816509
Thermus thermophilus (bacteria)4914980
Pseudomonas aeruginosa (bacteria)2414443
Staphylococcus aureus (bacteria)22136911
Bacillus subtilis (bacteria)4312971
Arabidopsis thaliana (thale cress)28126522
Escherichia coli K-12 (bacteria)135110919
Oryctolagus cuniculus (rabbit)2668311
Sus scrofa (pig)1768880
Saccharomyces cerevisiae S288C (yeast)15482920
Drosophila melanogaster (fruit fly)519059


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