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新數據登記以及註釋系統開放接受NMR和3DEM結構數據

wwPDB合作夥伴隆重推出新數據登記系統，全面支持使用3DEM，NMR和X射線，中子線和電子晶體學測定的各種結構數據。 請從下述網頁提交新數據：
http://deposit-next.wwpdb.org/deposition/

新系統實現了與EMDB和BMRB群集交互操作，可將原子坐標（PDB）文件與EM電子密度圖（EMDB）或核磁共振實驗數據（BMRB）同時登記，並同時發行PDB，EMDB以及BMRB編號。

請參考簡略教程
http://www.wwpdb.org/deposition/tutorial.

wwPDB於2014年1月推出新登記系統。作為第一階段，首先確立了X射線晶體學結構數據的登記與註釋系統。目前為止，已有超過12000件X射線結構數據通過新系統登記註釋，其中已公佈數據達6800件以上。

根據wwPDB專門委員會（wwPDB Task Force）的建議,^1,2,3 新系統對數據登記和註釋做了很多改進，比如配體情報的提取和檢驗，數據提交前後的原子坐標文件或實驗數據文件的替換，登記人和wwPDB編輯人員的交流方式等等。

至少到2016年上半年為止，原有數據登記工具（EMDep, ADIT-NMR, AutoDep）仍將接受新數據。

一旦新系統確認運行穩定,原有登記工具將被逐步淘汰。屆時對原有系統中未完成登記的數據,將提供一定的期間予以完成提交。此項手續已成功試用於2015年初,順利關閉了ADIT的X射線結構的登記。

【參考文獻】

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.