2016 Remediation of 3DEM Entries (wwPDB News)

OneDep deposition site is now accessible with HTTPS("secure"). Accesses to http are automatically redirected to https.

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Remediation of 3DEM Entries in the Protein Data Bank (wwPDB News)

AutoDep, ADIT-NMR and EMDep Deposition Systems Have Been Retired, Effective September 30th 2016 (wwPDB News)

News, Aug 31, 2016 - Yorodumi Docs" /> On 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
See this page for details. News, Aug 31, 2016 - Yorodumi Docs

A paper regarding Molmil, a molecular viewer developed by PDBj, has been published.

wwPDB Validation Server Upgrade (wwPDB News)

PDBj has started a service to link each PDBID to the database for Intrinsic Disordered proteins, IDEAL, which is developed by Nagoya University group.

Announcement: Map Volume Deposition to EMDB Will Be Mandatory for PDB Depositions of 3DEM models Starting September 6th, 2016 (wwPDB News)

The RDF version of SIFTS is now available at our FTP site ftp://ftp.pdbj.org/RDF/sifts/. SIFTS provides various annotations of protein sequences in the PDB such as the Gene Ontology, taxonomy (biological species), structural classifications (SCOP and CATH), enzyme codes, and correspondence with UniProt sequences, and its RDF version facilitates the integration of these data with RDF data from diverse sources by using the semantic web technologies.

Deposit ORCID and Grant Information with PDB Data (wwPDB News)

Access to wwPDB and RCSB PDB websites (wwPDB News)

The PDBeta web service has terminated.

Please download PDBeta application and use it in local. We'll continue to update it.

AutoDep Deposition System to Be Retired, Effective August 25^th 2016. ADIT-NMR and EMDep Deposition Systems to Be Retired, Effective September 30^th 2016. (wwPDB News)

Improved Worldwide Support for wwPDB Deposition, Validation, and Annotation (wwPDB News)

Designate Depositions for the CASP-12 Structure Prediction Competition (wwPDB News)

jV 4.5.1." />

PDBj announces the bug fix update of the molecular viewer jV 4.5.1. The difference from the previous version (4.5) is that the bug fix involved in writing static image into directories without permission.

New NMR and 3DEM Validation Reports for Archived PDB Structures (wwPDB News)

Ligand Validation Workshop Paper Published (wwPDB News)

The PDBj Mine2 relational database (RDB) now integrates the summary data of SIFTS developed by PDBe and UniProt. By combining PDBj Mine2 and SIFTS, the user can easily retrieve, using SQL, various annotations of protein sequences in the PDB such as the Gene Ontology, taxonomy (biological species), structural classification (SCOP and CATH), enzyme codes, and correspondence with UniProt sequences. For more information, please refer to the help page.
Please also refer to ftp site (ftp://ftp.pdbj.org/mine2/sifts/) to integrate PDBe's SIFTS into the PDBj Mine2 database.

Zika Virus Structure Released (wwPDB News)

wwPDB Deposition, Annotation, and Validation System To Support Suppression of Entry Author Lists and Titles (wwPDB News)

AutoDep, ADIT-NMR, EMDep Deposition Systems to Be Retired, Effective September 30^th 2016 (wwPDB News)

Updated X-ray Validation Reports for Archived PDB Structures Now Available (wwPDB News)

Coming Soon: New NMR and 3DEM Validation Reports for Archived PDB Structures (wwPDB News)

The new version (4.5) of jV molecular viewer provided by PDBj is now available. From this version, it can load and save in mmCIF format for small molecules (chem_comp mmCIF).

Coming soon: Updated X-ray Validation Reports for Archived PDB Structures (wwPDB News)

wwPDB新数据登记以及注释系统开放接受NMR和3DEM结构数据

wwPDB合作伙伴隆重推出新数据登记系统，全面支持使用3DEM，NMR和X射线，中子线和电子晶体学测定的各种结构数据。 请从下述网页提交新数据：
http://deposit-next.wwpdb.org/deposition/

新系统实现了与EMDB和BMRB群集交互操作，可将原子坐标（PDB）文件与EM电子密度图（EMDB）或核磁共振实验数据（BMRB）同时登记，并同时发行PDB，EMDB以及BMRB编号。

请参考简略教程
http://www.wwpdb.org/deposition/tutorial.

wwPDB于2014年1月推出新登记系统。作为第一阶段，首先确立了X射线晶体学结构数据的登记与注释系统。目前为止，已有超过12000件 X射线结构数据通过新系统登记注释，其中已公布数据达6800件以上。

根据wwPDB专门委员会（wwPDB Task Force）的建议,^1,2,3 新系统对数据登记和注释做了很多改进，比如配体情报的提取和检验，数据提交前后的原子坐标文件或实验数据文件的替换，登记人和wwPDB编辑人员的交流方式等等。

至少到2016年上半年为止，原有数据登记工具（EMDep, ADIT-NMR, AutoDep）仍将接受新数据。

一旦新系统确认运行稳定，原有登记工具将逐步淘汰。届时对原有系统中未完成登记的数据，将提供一定的期间予以完成提交。此项手续已成功试用于2015年初，顺利关闭了ADIT的X射线结构的登记。

【参考文献】

1. A New Generation of Crystallographic Validation Tools for the Protein Data Bank, Randy J. Read, Paul D. Adams, W. Bryan Arendall III, Axel T. Brunger, Paul Emsley, Robbie P. Joosten, Gerard J. Kleywegt, Eugene B. Krissinel, Thomas Lütteke, Zbyszek Otwinowski, Anastassis Perrakis, Jane S. Richardson, William H. Sheffler, Janet L. Smith, Ian J. Tickle, Gert Vriend and Peter H. Zwart. (2011) Structure 19: 1395-1412 doi: 10.1016/j.str.2011.08.006
2. Outcome of the First Electron Microscopy Validation Task Force Meeting, Richard Henderson, Andrej Sali, Matthew L. Baker, Bridget Carragher, Batsal Devkota, Kenneth H. Downing, Edward H. Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff, Wen Jiang, Steven J. Ludtke, Ohad Medalia, Pawel A. Penczek, Peter B. Rosenthal, Michael G. Rossmann, Michael F. Schmid, Gunnar F. Schröder, Alasdair C. Steven, David L. Stokes, John D. Westbrook, Willy Wriggers, Huanwang Yang, Jasmine Young, Helen M. Berman, Wah Chiu, Gerard J. Kleywegt, and Catherine L. Lawson. (2012) Structure 20: 205-214 doi:10.1016/j.str.2011.12.014
3. Recommendations of the wwPDB NMR Validation Task Force, Gaetano T. Montelione, Michael Nilges, Ad Bax, Peter Güntert, Torsten Herrmann, Jane S. Richardson, Charles D. Schwieters, Wim F. Vranken, Geerten W. Vuister, David S. Wishart, Helen M. Berman, Gerard J. Kleywegt, and John L. Markley. (2013) Structure 21: 1563-1570 doi:10.1016/j.str.2013.07.021

[ wwPDB News ]

jV 4.4.5, signed with updated certification, has released. The certification used to sign jV 4.4.4 will expire on Jan. 21, 2016. After expired, it doesn't work as applet. So we recommend for all administrator of web servers that include jV applet pages to update jV to 4.4.5. To see details of the changed points, see the Release note section of the jV manual." /> The jV 4.4.5, signed with updated certification, has released. The certification used to sign jV 4.4.4 will expire on Jan. 21, 2016. After expired, it doesn't work as applet. So we recommend for all administrator of web servers that include jV applet pages to update jV to 4.4.5. To see details of the changed points, see the Release note section of the jV manual.

The Protein Globe service has been discontinued from January 2016.