This page lists the files within the PDBj data archive. Information regarding data retrieval is written on the PDBj download page. Files within the data site efsite/data-web/${entryId}.mpbf.gz pdb_versionedShared between all wwPDB members data entries ...

CiCLE workshop: sample evaluation for cryo-EM Outline：For obtaining high-resolution structures by single particle cryo-EM suitable sample evaluation and sample preparation is essential. An important aspect of sample evaluation is the effective use of ...

The wwPDB validation reports provided in the OneDep system now have additional validation for electron microscopy (EM) maps to help users identify potential discrepancies in their data. The updated wwPDB validation reports in the OneDep system now ...

This page provides some examples of SQL queries that can be executed from the PDBj Mine interface at https://pdbj.org/rdb/search. You can use these samples at SQL Search of PDBj Mine or PDBj Mine:REST API. Documentation describing the SQL schema can be ...

The wwPDB partners are pleased to announce an improved mechanism for the resolution of digital object identifiers (DOIs) associated with released PDB entries. We have launched new wwPDB landing web-pages for each released PDB entry. These pages present ...

The service of Encyclopedia of Protein Structures (eProtS) is now under maintenance.

On 24th Sep, we will hold a luncheon seminar at the 57th Annual Meeting of the Biophysical Society of Japan in Miyazaki. Details are the following: Date 24th September 2019 (Tue) 11:30 - 12:20 (JST) Venue Seagaia Convention Center, Room G (IVORY) ...

We'll exhibit a booth at the 29th Science Festa Osaka, which is a scientific event for young people. The exhibition day of our booth is only on 8/18 (Sun). We are going to exhibit the following menus: - Explanation of the basic for proteins - ...

We are pleased to announce the availability of PDB versioning, allowing depositors to update their entries while retaining the same PDB accession code. Depositors can now submit new coordinates for existing entries. Initially, this is limited to PDB ...

Q) When are PDB entries released or updated? Can I download exactly the same PDB data from RCSB PDB, PDBe or PDBj? Is the update schedule different among them? A) The PDB data is updated on every 00:00 UTC (= 09:00 JST) of Wednesday at every site of ...

Q) Where is the XML Schema for the XML document for PDB? A) Please refer the following links for XML Schemas for PDBML and PDBMLadd. - PDBML - PDBMLadd [Back to the question list]

On October 4th, 2017, the wwPDB introduced a versioning system to enable depositor-initiated or wwPDB-initiated updates to previously released PDB entries while retaining the same PDB accession code. A new FTP repository, now hosts versioned structural ...

From today, July 1st 2019, submission of PDBx/mmCIF format files for crystallographic depositions to the PDB is mandatory. PDBx/mmCIF is now the only format accepted for deposition of PDB structures resulting from macromolecular crystallography (MX), ...

wwPDB OneDep System wwPDB OneDep system supports X-ray, EM and NMR structures. - Help for deposition wwPDB site: Tutorials wwPDB site: wwPDB OneDep System wwPDB site: wwPDB OneDep System FAQ wwPDB site: 5 Easy Steps to PDB Deposition with OneDep (PDF ...

[PDBx/mmCIF] The PDBx/mmCIF format is modified format based on CIF (a file format used to describe crystal structures) and has been adapted for macromolecules. Both PDBx/mmCIF as well as CIF are based on the STAR format. The PDBx/mmCIF format will become ...

[PDBML: XML for PDB] PDBML is one of the canonical XML formats converted from the PDBx/mmCIF format into XML. This format was first introduced in the following article: PDBML: the representation of archival macromolecular structure data in XML. ...

PDBML-noatom files are the same as PDBML files except that there is noatom_siteCategoryelement. This means there are no atomic coordinates saved in the PDBML-noatom files. The XML schema for the PDBML-noatom file is the same as the PDBML file provided at ...

- Search Services - PDBj Mine - SQL Search - Get the chain IDs (auth_asym_ids and lable_asym_ids), entity IDs, entity names and type of chain (polymer or not) for PDB entiry 4uv7 This search can be run from here. WITH t1 AS (SELECT DISTINCT e1.pdbid, ...

Our recent update to the wwPDB validation reports provides much clearer validation information for ligands. We now include 2-dimensional diagrams of ligands, highlighting geometric validation criteria and, for structures determined by crystallography, ...

All of us at wwPDB were deeply saddened to hear of the recent passing of Prof. Michael G. Rossmann and our condolences go out to his family and friends at this time. Michael contributed so much to the field of structural biology and was a great supporter ...

The GIRAF service terminated on 30th April 2019. Thank you for using so long. [The URL] https://pdbj.org//giraf/ [Introduction to GIRAF] GIRAF is a similarity search service for ligand binding sites available at https://pdbj.org//giraf/. For a given ...

The GIRAF service will terminate on 30th April 2019. Thank you for using so long.

A new publication in Acta Cryst D announces the mandatory submission of PDBx/mmCIF to the PDB for crystallographic depositions. (wwPDB news)

A job is opening for a founding director of Protein Data Bank China (PDBc), with the primary task of establishing structure archiving activities in China. (wwPDB news)

With this week's update, the PDB archive has passed the milestone of 150,000 entries, and now contains a total of 150,145. (wwPDB news)