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)

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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 등록・주석 시스템을 사용하여 NMR과 전자현미경법 (3DEM)으로 결정된 구조를 등록 할 수 있게 되었습니다.

wwPDB등록・주석 시스템을 사용하여 전자현미경법(3DEM), NMR, X선, 중성자선, 전자선결정 해석으로 결정된 구조를 등록 할 수 있게 되었습니다. 현재, 아래의 사이트에서 등록 가능합니다.
http://deposit-next.wwpdb.org/deposition/

새로운 시스템은 EMDB와 BMRB에 연결되어 있기 때문에 PDB의 원자좌표 등록과 EMDB에서의 EM전자밀도 맵의 등록 또는 BMRB의 NMR 데이터의 등록을 함께 실시할 수 있습니다. 구조가 등록되면, PDB, EMDB, BMRB의 액세스 코드가 발행됩니다.

개요에 대해서 아래의 튜토리얼을 참조하십시오.
http://www.wwpdb.org/deposition/tutorial (English)
http://pdbj.org/help/wwpdb_dep_tutorial (Korean)

2014년1월에 wwPDB는 국제적으로 일치된 구조 데이터의 등록 및 주석 시스템을 발표하기 위한 제1단계로써, X선 결정구조를 대상으로 새로운 등록· 주석 시스템을 시작했습니다. 12, 000건 이상의 X선 결정구조가 새로운 시스템을 사용해서 등록 되었고, 주석 처리가 되었습니다. 그 중에서 6, 800건 이상이 이미 공개되어 있습니다.

X선/전자현미경법/NMR을 통합한 포괄적인 등록·주석 시스템에는 아래와 같은 특징이 새롭게 추가되거나 개량되었습니다. wwPDB의 전문임원회(wwPDB Task Force)의 권장에^1,2,3 따른 검증 레포트의 생성, 리간드 정보의 검토기능 개선, 등록 전후의 좌표와 실험 데이터의 변경 기능, 등록자와 wwPDB 주석자간의 커뮤니케이션 절차의 개선등.

적어도 2016년 전반에 실시되는 새로운 등록에 있어서, 새로운 시스템을 사용하더라도 종래의 등록 툴(EMDep, ADIT-NMR, AutoDep)의 사용도 가능합니다.

새로운 시스템이 안정화 되어서 가동하게 되면, 기존의 등록 툴은 등록 도중의 세션을 완료하기 위한 충분한 시간을 준 뒤에 종료 될 예졍입니다. 이 절차는 2015년 초에 실시된 X선 결정구조 등록 ADIT 시스템의 종료 절차와 동일합니다.

【참고 문헌】

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.

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