Paper Published "How Community Has Shaped the Protein Data Bank" (wwPDB News)

New wwPDB X-ray structure validation reports support depositors, journal editors and referees The wwPDB partners are pleased to announce that new, considerably more informative X-ray structure validation reports are now being provided to depositors as ...

Structural Life Science - 7th International Conference on Structural Genomics (ICSG2013-SLS) will be held in Sapporo, Japan, July 29th - August 1st, 2013. PDBj will introduce activities of PDBj and wwPDB in a booth display.

The presentation materials from the 11th Japan-Korea-China Bioinformatics Training Course & Symposium (June 17-18, 2013) are available for download.

Celebrating 10 Years of the wwPDB

10,000 NMR structure milestone reached The wwPDB is excited to announce that the number of structures available in the PDB archive determined using Nuclear Magnetic Resonance (NMR) spectroscopy has passed the 10,000 mark. NMR and the PDB Since the ...

The following seminar is finished. The 11th Japan-Korea-China Bioinformatics Training Course & Symposium - Period: June 17th (Mon.), 18th (Tue.) - Venue: Soochow University, Suzhou, China We are pleased to announce that "The 11th Japan-Korea-China ...

Two complete HIV-capsid structures, both of unprecedented size, are described in this week's issue of Nature and released in the Protein Data Bank (PDB; wwpdb.org). This represents a significant advance in the field of structural biology and a milestone ...

[PDBj Mine search results right side menu] After searching for PDBj Mine using either the quick search bar or the advanced search, the results will be displayed within your browser. The center of the screen holds the search results, while on the right side ...

In order to meet the challenges of ever greater numbers of PDB depositions, involving ever larger and more complex structures, often determined using multiple methods, the Worldwide Protein Data Bank partners (wwPDB: http://wwpdb.org/) are developing a ...

90,000 entries released: With the May 1, 2013 update, 90,206 PDB entries became available in the archive.

The Biologically Interesting Molecule Reference Dictionary (BIRD) for Peptide-like Antibiotic and Inhibitor Molecules The wwPDB's Biologically Interesting molecule Reference Dictionary (BIRD) describes antibiotics, peptide inhibitors, and other complex ...

The Job Manager lists all processing and completed jobs. Currently only the Structure Navigator and the PDBeta services use the Job Manager. In the future other services will be added. Once a job has been finished, the Job Manager will notify the user of ...

3D molecular view of vibration The molecules fluctuating in each of the 10 lowest-frequency normal modes can be displayed on the 3D molecular viewers, jV (PDBj) and Jmol. (1) Displacement vectors Fluctuations of the molecules are displayed on the ...

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ProMode-Elastic is a database of normal mode analysis (NMA) of PDB data using a program PDBETA we have developed. PDBETA is a program of Elastic-network-model based normal mode analysis in Torsional Angle space for PDB data. PDBETA can describe molecular ...

The latest version of jV, jV4.3, has been released. Please download the newest version from here. See Release note for more details.

[About Asymmetric Unit] Asymmetric Unitis used in either meaning of Crystal asymmetric unit or Non-Crystallographic asymmetric unit. Crystal Asymmetric Unit The crystal asymmetric unit is the smallest portion of a crystal structure to which symmetry ...

The new format, v.1.9.0, for the EMDB header file (XML file associated with each map) has been released. All EMDB header files in the FTP archive have been updated to new version (ftp://ftp.pdbj.org/pub/emdb/structures/EMD-/header/emd-.xml) The ...

The number of structures annotated by PDBj has reached 20,000. PDBj has annotated 20,000 structures since we began annotating PDB entries in 2000. We are grateful to all depositors and wwPDB members for this great accomplishment. Statistics for PDB ...

Remediation of Structure Factor Data and Release Plan The wwPDB has reviewed structure factor files in the archive for format consistency and correspondence with coordinate data. As a result, around 43,800 structure factor files have been updated to ...

EMDB header format to be updated to v.1.9.0. On 16 January 2013, the EMDB archive plans to adopt an updated format, v.1.9.0, for the entry header file (XML file associated with each map). This means that EMDB header files distributed from wwPDB partner ...

New Reference Dictionary for Biologically Interesting Molecules (BIRD) Released on FTP As previously announced, BIRD has been released on the PDBj/wwPDB FTP server at the following sites. For more details about BIRD, please see the news of Oct 19. ...

Announcement: Experimental Data Release Policy Clarification Effective February 6, 2013, coordinates and experimental data deposited in the PDB will follow the same release status. ( wwPDB News... ) Questions should be sent to info@wwpdb.org.