[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

-
Search query

Keywords
Structure methods
Author
Journal
IF

-
List of structure papers

Showing 1 - 20 of 111,548 items (all data)

-
Staphylococcus aureus MazF in complex with nanobody 4

-
De Novo Design of Integrin alpha5beta1 Modulating Proteins for Regenerative Medicine

-
Cocrystal of PPARg LBD with NFKBIB / IKBB peptide containing N-anchor motif LxxLL and agonist GW1929

-
Poc1 bridges basal body inner junctions to promote triplet microtubule integrity and connections.

-
Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies

-
Formerly degenerate seventh zinc finger domain from transcription factor ZNF711 rehabilitated by experimental NMR structure

-
SARS CoV-2 nsp10 in complex with theExoN domain from nsp14

To Be Published,
Fisher, S.Z.
Methods: X-ray diffraction

-
Deciphering the SAM- and Metal-Dependent Mechanism of O-Methyltransferases in Cystargolide and Belactosin Biosynthesis: A Structure-Activity Relationship Study

-
SARS CoV-2 nsp10 in complex with the ExoN domain from nsp14

To Be Published,
Fisher, S.Z.
Methods: X-ray diffraction

-
Coxsackievirus B3 3C protease in C121 spacegroup

-
The Structure of Spiroplasma Virus 4: Exploring the Capsid Diversity of the Microviridae

-
Crystal structure of marine sulfatase (OpSulf1) from Ochrovirga pacifica

-
Role of Water in the Selective Complexation of Rare Earth Elements by Lanthanide Binding Tag Peptides

-
Nucleotide independent as well as ATP-hydrolysis driven steps of Rea1 Linker remodelling drive the removal of assembly factors from pre-ribosomal particles

-
The HIV protease inhibitor amprenavir binding to the active site of Cryphonectria parasitica endothiapepsin

-
Characterization of structural, biochemical, pharmacokinetic, and pharmacodynamic properties of the LSD1 inhibitor bomedemstat in preclinical models.

-
Bio-SANS investigation of fungal loosenins reveal substrate dependent impacts of protein action on inter-fibril distance and packing order of cellulosic substrates

-
Polyphosphate bound alpha-synuclein fibril

To Be Published,
Tao YQ / Liu C / Li D
Methods: EM (helical sym.)

-
Structural Insights into the NMN Complex of Nicotinate Nucleotide Adenylyltransferase from Enterococcus faecium via Co-Crystallization Studies

-
Structural insights into the substrate recognition and catalytic mechanism of a beta,kappa-carrageenase from Wenyingzhuangia funcanilytica

To Be Published,
Chang, Y. / Chen, F.
Methods: X-ray diffraction

Pages:

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more