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News on 2009-02-13

... to be Released March 18 , 2009 The wwPDB will release a newly standardized and enhanced version of the entire PDB archive ... file format documentation, please see www.wwpdb.org/docs.html. A time-stamped snapshot of the PDB archive before this release will ...

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2020 July is the 20th anniversary of PDBj.

... when PDBj locally processed the 1st deposition to Osaka University, as a part of the JST-BIRD project. While in 2000, only 157 ... , Asia and Oceania were assigned to PDBj, but due to a dramatic increase of depositions from Asia, especially main land China, ...

Molmil 2 has become the default viewer of PDBj web interface from Nov. 1st, 2018

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[wwPDB] Improved Depositor Experience Using ORCiD

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[wwPDB] Improve Your Previously-Released Coordinates AND Keep Your Original PDB ID: Phase II

... archive FTP (ftp.wwpdb.org). All major versions of a PDB structure will be retained in the versioned FTP archive ... to atomic coordinates, polymer sequence, or chemical description trigger a major version increment, while changes to any other categories are ...

News on 2014-12-24

Beginning at 9:00 a.m. on January 27, 2015 (JST) crystal structures should be submitted using ... . Improvements to this system are regularly incorporated based on user feedback. As a result of this successful release, RCSB PDB and PDBj will only accept ...

confidentiality of deposition data - FAQ

... deposited information could leak out from the PDB before release? A) The deposited data is managed under strict security constraints ... leaking out. Only our annotation staff who are bound by a non-disclosure agreement have access to the data. [Return ...

Deposition and Release of PDB Entries Containing Large Structures

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RMSD

RMSD stands for root mean square deviation. It is a commonly used measure of dissimilarity or error in protein structure. For ... two sets of points and a mapping between those points the RMSD is defined to be the square ...

sequence-representative

... scores for all pairs of structures. The pairs which score above a certain threshold (Sequence identity30% and E-value0.1) arelinked. ... structure with the greatest number of links is chosen, and a new cluster defined with it as the representative and all of ...

PDBML

... (categories), refer the PDBx/mmCIF dictionary. The file name of a PDBML file is pdbid.xml. For example, 1a00.xml, 1gof. ... ” files contain only atomic coordinates and related information, but in a more concise format than the atom_site element of PDBML. This ...

CIF --> JSON converter

... /mmJSON. Besides PDBx/mmCIF, other STAR formatted files should also work. Select a file below and then click on "Convert". Note that the files will ...

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News on 2015-12-18

... can search the wwPDB/RDF data along with other data resources through a SPARQL endpoint. See RDF Portal for NBDC for more details." /> ... the wwPDB/RDF data along with other data resources through a SPARQL endpoint. See RDF Portal for NBDC for more details.

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Chemical shift

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[wwPDB] PDB50: Registration Open for Virtual Event

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[wwPDB] wwPDB EM Validation Reports Now Publicly Available

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[wwPDB] Consistent Format for Validation and Coordinate Data

... Archives. The new PDBx/mmCIF reports are easier to interpret. They contain a high-level summary and offer easier access to residue-level information. Data ...

News on 2004-09-01

We start a new service, Sequence Navigator, to allow searching for homologous proteins using the amino acid sequence.

News on 2010-07-13

The latest version of jV (jV3.8), the molecular graphics viewer developed by PDBj, has been released. A new functional command "displayatom on/off" has been added, which provides various display methods easily. Please download the newest version from here.

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PDB entries from 2024-06-26

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