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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 ...

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[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.

The videos for wwPDB Foundation Outreach Seminar, which was held in Osaka on October 13, have been released on YouTube. ( more... )

The CCP4 workshop was held in Fukuoka on November 2, 2012. The presentation materials are available for download.

September 16, 2005 [About] Functional Details page A Functional Details page has been prepared so as to display the functional information of individual proteins: Biological process, Cellular location, and Biochemical function, with the residue-specific ...

New Reference Dictionary for Biologically Interesting Molecules to be Released on FTP December 2012 The wwPDB has reviewed the representation of peptide-like antibiotic and inhibitor molecules in the PDB archive. As a result, a new reference dictionary ...

wwPDB Foundation Outreach Seminar was held in Osaka on October 13, 2012. The presentation materials are available for download.

Public release of wwPDB/RDF. PDBj has been providing RDF(Resource Description Framework)-formatted PDB data based on the pdbj.org domain. From now on, the URLs of PDB/RDF data will be provided from the rdf.wwpdb.org domain. The following are examples of ...

The URLs for ftp/rsync services have been changed as follows. The previous URLs are still available for a while. - pdb.protein.osaka-u.ac.jp -> ftp.pdbj.org - snapshots.pdbj.org -> snapshots.pdbj.org The ftp command will connect to an anonymous ftp ...

[Chemical Shift] NMR chemical shift file is mandatory when submitting NMR entries to the PDB after December 6, 2010. Deposition systems support the deposition of chemical shift data in NMR-STAR (V3.1) format and perform checks to confirm the ...

[NMR restraints] NMR restraints file is required to deposit NMR structures after February 1, 2008. (version 1) There is no restriction on the format for the NMR restrains data. (Output format of Discover, Emboss, CYANA or X-PLOR is recommended) The ...

[Structure factors] Structure factors amplitudes/intensities in mmCIF format Structure factors file is required to deposit X-ray diffraction structures after February 1, 2008. For descriptions and examples of specific tokens, please refer to the ...

[NER] NER stands for the Number of Equivalent Residues [1] is an empirical measure of the similarity of two protein structures. The NER superposition corresponds to the rotation and translation that maximizes the NER score. The NER score is bounded ...

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