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

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Name, Taxonomy-ID, or Keywords:

e.g. E. coli, ebola, influenza, cow, crab-eating macaque, spinach, peanut, cobra, pyrococcus

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Showing 1 - 20 of 7,052 items

Homo sapiens (human)122739345181
Escherichia coli (E. coli)593779348
Mus musculus (house mouse)285601739
synthetic construct (others)304321827
Rhodococcus sp. HI-31 (bacteria)0318
Bos taurus (cattle)280274318
Staphylococcus aureus (bacteria)18132711
Streptococcus pneumoniae (bacteria)1455510
Escherichia coli K-12 (Escherichia coli in molecular biology)8693210
Phaeodactylum tricornutum (eukaryote)079
Leishmania braziliensis (eukaryote)079
Chlorobaculum tepidum TLS (bacteria)0159
Saccharomyces cerevisiae S288C (yeast)1207109
Xenopus laevis (African clawed frog)592838
Drosophila melanogaster (fruit fly)468637
Saccharomyces cerevisiae (baker's yeast)65433957
Bradyrhizobium diazoefficiens USDA 110 (bacteria)0156
Gallus gallus (chicken)3815886
Candidatus Kuenenia stuttgartiensis (bacteria)0105
Desulfovibrio alaskensis G20 (bacteria)0135


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