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News on 2005-04-28

The data, text, and figures on this site are free to the public. When you make use of the contents of this site, please cite as "Protein Data Bank japan: PDBj". The ftp archival site is provided at ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/ .

News on 2011-12-20

EM Data Bank to join the PDB archive The EM Data Bank (EMDB), the primary archive for experimentally-determined maps obtained using three-dimensional electron microscopy methods, will join the PDB archive on March 7, 2012. ( wwPDB News... )

Launch of our renewed EDMap service

... /. For the wwPDB data, the maps are available at: - /pub/pdb/validation_reports/*/*/*_validation_fo-fc_map_coef.cif.gz - /pub ... /pdb/validation_reports/*/*/*_validation_2fo-fc_map_coef.cif.gz While the ...

[wwPDB] Remediation of crystal structures deposited in non-standard coordinate frames

A total of 268 structure entries deposited to PDB in a non-standard coordinate frame or space ... /matrices remain accessible/downloadable as the previous major version in PDB's versioned archive. Coordinate frame-transformed myoglobin 1MBO coordinates with ...

[wwPDB] Congratulations to Poster Prize Winners

... Shelter Island High School, Molecular Dynamics Simulation of 6PEY.pdb a Novel Mutation in the Enzyme Methylenetetrahydrofolate Reductase - Best ... is celebrating the 50th Anniversary of the PDB throughout 2021 with symposia, materials, and more. [ wwPDB ...

NMR restraints

... deposited restraints data is released as is with a part of PDB header on the top of the file and the coordinates of ... files are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom-level correspondences to the ...

Structure factors

... examples of specific tokens, please refer to the mmCIF dictionary of RCSB PDB at: http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Categories/refln.html

2020 July is the 20th anniversary of PDBj.

... 2001 due to the kind technical and scientific help from RCSB PDB, and processed 602 entries in 2002. With the formation of ... eF-Site and ProMode, introducing new formats such as PDBMLplus and PDB/RDF, and developed original tools such as Molmil or MagRO. We ...

[wwPDB] New Publication: PDBx/mmCIF Ecosystem

... data representation for structural biology data that is critical to the PDB archive. It describes file standards and governance, and summarizes software ... format as the foundation of the modern Protein Data Bank (PDB) archive (wwPDB.org). [ wwPDB News ]

News on 2007-08-01

The PDB archive has been remediated and is available starting August 1, 2007 from ftp://ftp.wwpdb.org/ and from our mirror site: ftp://pdb.protein.osaka-u.ac.jp/v3/.

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News on 2008-11-25

... Guide Version 3.20 Beginning December 2, 2008, all newly-released PDB entries will follow PDB File Format Contents Guide Version 3.20 ( PDF | HTML ). This ...

[wwPDB] Distribution of Electron Microscopy metadata in PDBx/mmCIF file format

... files in the archive will bring parity between EMDB and PDB (EM experimental data vs 3D structures) in the way ... /structures/ - wwPDB: https://files.wwpdb.org/pub/emdb/structures/ - RCSB PDB (US): https://files.rcsb.org/pub/emdb/structures/ - PDBe (UK): ...

News on 2008-09-16

... and procedures related to data processing and annotation. The result is a PDB Contents Guide Version 3.2 that more fully describes the ... PDB file format. This document is available as a PDF and in HTML, ...

Interactive Tutorial Series

... by doing the PDBj Mine quick search tutorial. Of course the PDB entry pages have also received a facelift and offer a couple ... new features. Find out how more by doing the PDBj Mine PDB Explorer tutorial. The Advanced search page has also been updated and ...

[wwPDB] Updated Annotation and Standardization of Peptide Residues

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[wwPDB] wwPDB Charter: Full and Associate Members

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PDBj FTP Archive reorganization

... follows: (1) ftp.pdbj.org wwPDB common area for /pub (i.e., pdb and emdb) only (same as wwPDB's and RCSB's core FTP ... -versioned.pdbj.org The same as before, this only contains the versioned PDB data (3) data.pdbj.org This contains both (1) and (2), and ...

Functional annotation example

... At the time the structure was solved, there were no PDB entries with significant sequence homology, however conservation and geometry of ... pathway. Currently, the closest match to 1uan in the PDB is 2ixd, a putative deacetylase from Bacillus cereus that was ...

[wwPDB] Paper Published on NextGen Archive

... access to integrated annotations and enriched structural information for PDB data: NextGen Archive: Centralising Access to Integrated ... provided in the structure model files in the PDB main archive. The inclusion of UniProtKB numbering facilitates ...

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[wwPDB] Additional EM map validation now available through OneDep

... however in future will be provided for entries throughout the PDB and EMDB archives. The process includes an analysis of ... about potential limitations of the data in both the PDB and EMDB. Additional information about validation reports for EM ...

Similarity Search for Ligand Binding Sites at Atomic Resolution

... protein structure, GIRAF searches for ligand binding sites in the PDB that are structurally similar to substructures of the query. As ... a query, you can specify a PDB ID or upload your own PDB-formatted file. For more information, please refer ...

The 12th AsCA will be held in Hong Kong from 7 to 10 December. Haruki Nakamura, Head of PDBj will give a poster presentation to introduce PDBj's web services and our latest activities.

... Protein Research, Osaka University) "Modifications to the Protein Data Bank (PDB)" - Date&Time: Sunday 8 December 10:50-11:15 ... , Osaka University) - "Modifications to the Protein Data Bank (PDB)" - Poster Presentation Date&Time: Monday 9 December 16:15-18 ...

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