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 ...

Structural Genomics (SG) refers to the structural determination of all the proteins in a particular genome. More generally, SG has come to mean the effort to solve a representative set of protein structures, from which models of all proteins can be built ...

http://bmrbdep.pdbj.org/index_en.html BMRB is a database for NMR data of peptides, proteins and nucleic acids, and is maintained by BioMagResBank at the University of Wisconsin-Madison. This website is maintained by PDBj-BMRB group at Institute for ...

URL： https://pdbj.org//spanner/ Spanner is a structural homology modeling program―that is, it threads a specific amino-acid sequence onto a specific PDB structure, patching up the gaps as best it can. To create a model, you must provide a template ...

[Contents] - Contents - URL - What is CRNPRED? - How to use CRNPRED server - How should I interpret the results? I don't receive any email from CRNPRED! - How should I interpret the results? - I don't receive any email from CRNPRED! - How CRNPRED ...

Sequence representative lists are generated by first computing BLAST scores for all pairs of structures. The pairs which score above a certain threshold (Sequence identity30% and E-value0.1) arelinked. The set is first clustered using single-linkage ...

[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 ...

RMSD stands for root mean square deviation. It is a commonly used measure of dissimilarity or error in protein structure. For two sets of points and a mapping between those points the RMSD is defined to be the square-root of the average of the squared ...

[Alignment] In bioinformatics, alignment refers to a mapping betweenequivalentamino acids (in the case of proteins) or nuceotides (in the case of DNA or RNA). In the case of proteins, we usually consider two basic types of alignment, sequence alignment ...

[Structural Superposition] The term structural superposition refers to rotations and translations performed on one molecular structure to make it match another structure or structures. Inherent in the definition of structural superposition is an assumed ...

[PDB ID] A PDB ID is a unique 4-character code for each entry in the Protein Data Bank. The first character must be a number between 1 and 9, and the remaining three characters can be letters or numbers.

BLAST stands for Basic Alignment Search Tool. Because of its speed and the reliability, BLAST is a very widely used program for sequence alignment. The statistical significance of a BLAST alignment is given by its expectation value or E-value. The E-value ...

MAFFTash URL: http://sysimm.org/MAFFTash// - Overview - Usage - Methods - Structural alignment Sequence alignment - Structural alignment - Sequence alignment - Prep-MAFFTash - MAFFTash Output - References [Overview] MAFFTash is a server that ...

PDBML-extatom files contain atomic coordinates in a "simplified" format. The XML schema for PDBML-extatom format is provided at: - https://pdbj.org//schema/pdbx-v40-ext.xsd And can also be viewed using our interactive XML viewer. In the canonical PDBML ...

In this tutorial, we provide explanation about the SeSAW, one of the service of PDBj. See also the SeSAW documentation about basic things such as used technique. - Submitting PDB entries to SeSAW - Submitting structures to SeSAW - Experimental ...