BMRBj (Biological Magnetic Resonance Data Bank Japan) at Osaka University supported by JST-NBDC (Japan Science and Technology Agency - National Bioscience Database Center) contributes to the community for Biomolecular NMR by collection, annotation, validating and archiving experimental NMR data in collaboration with wwPDB (Worldwide Protein Data Bank). Our mission is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of biomolecular NMR spectroscopy. Please deposit your NMR structure and related NMR parameters through our deposition sites; OneDep, BMRBdep, SMSDep. The released data are available from our BMRB mirror server. Please try our new search service above which allows you to quickly find rich information of biomolecule such as function, sequence, structure, NMR data as well as interaction in multiple databases including BMRB, PDB, EMDB, UniProt, IntAct, BMRB-Metabolomics and Ligand Expo.
The article on validation of structural model in PDB using NMR restraints has been published in Structure.
We attended BioHackathon 2023. The preprint of outcomes at the meeting has been published at BioHackrXive.
We are pleased to announce the release of corrected/combined NMR data files for existing NMR entries of the PDB Core Archive. wwPDB NEWS
A generation tool of alternative wwPDB validation information, pdbx-validation v4.4.29.
A database replication tool based on XML Schema, xsd2pgschema v4.4.7/5.3.7, is available.
The article about activities of BMRB/BMRBj groups has been published in Nucleic Acid Res.
A database replication tool based on XML Schema, xsd2pgschema v4.4.3/5.3.3, is available.
A generation tool of alternative wwPDB validation information, pdbx-validation v4.4.14.
A plot showing well-defined regions has been added to the content for combined NMR restraints.
The article about activities of BMRBj group has been published in Protein Science.
Incorporated AlphaFold Protein Structure Database sequence information as BLAST search results for each BMRB entry.
Tools for BMRB/XML and BMRB/RDF are update. The namespaces of BMRB/XML and BMRB/RDF will be changed respectively.
A nmrML converter for BMRB metabolomics entries, BMSxNmrML v1.3.0, is available.
Depositor can submit a release request for an On-Hold entry from the author view page by specifying PubMed ID of the primary citation.
Graphical content for the chemical shift validation reports is available.
We released chemical shift validation reports of all BMRB entries in JSON format. The schema is the same as for the combined NMR restraints report file.
Depositor can access refreshed author view page for uploaded or processed data files. The page contains detailed validation information and graphically represented summary content.
RCI and derived parameters (S2, NMR RMSD) plots are added as graphical contents for the NMR combined restraints.
We have changed our group name to BMRBj (Biological Magnetic Resonance Data Bank Japan), formerly kwnon as PDBj-BMRB. We look forward to working with you.
Entries with extended PDB and CCD ID codes will be distributed in PDBx/mmCIF format only. wwPDB NEWS
A database replication tool based on XML Schema, xsd2pgschema v4.2.3/5.1.3, is available.
Revised statistics page on BMRB entries is accessible.
Graphical content for NMR combined restraints of PDB/BMRB entries is available.
A generation tool of alternative wwPDB validation information, pdbx-validation v4.4.4.
A database replication tool based on XML Schema, xsd2pgschema v5.0.0, is available, which requires JDK14 or later.
A generation tool of alternative wwPDB validation information, pdbx-validation v3.0.0, is available, which supports NMR restraint validation.
We released a JSON Schema for the combined NMR restraints report file, which contains restraint statistics and diagnostic information.
We released an archive of combined NMR restraints (CS+MR) associated with PDB entries in both NMR-STAR and NEF formats. Polymer sequence, atom nomenclature and restraint data have been checked with the coordinate and remediated on the best effort basis. See also restraint statistics and diagnostic information of the combined NMR restraints reported in each JSON file. As of now, the archive contains 2463 valid NEF restraint files, which meet OneDep deposition requirements.
New Deposition server BMRBdep now available. ADIT-NMR will stop accepting new sessions on Sep 1st, and will stop allowing the completion of existing in-progress depositions on Dec.
The first PDB entries, 7JIA and 7JIY deposited by the NMR unified data, have been released.
A generation tool of alternative wwPDB validation information, pdbx-validation v2.0.16, is available.
We have added content on emerging Coronavirus infectious disease (COVID-19) caused by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
A database replication tool based on XML Schema, xsd2pgschema v4.1.4, is available.
OneDep began accepting upload of NMR experimental data as a single file, either in NMR-STAR or NEF format.
A generation tool of alternative wwPDB validation information, pdbx-validation v2.0.3, is available, which supports EM map/model validation.
The article about BMRB has been published in Method Mol. Biol.
As of March 2020 the OneDep system will begin accepting upload of NMR experimental data as a single file, either in NMR-STAR or NEF format. wwPDB NEWS
A generation tool of alternative wwPDB validation information, pdbx-validation v2.0.1, is available, which supports EM map/model validation.
A database replication tool based on XML Schema, xsd2pgschema v4.0.5, is available.
A generation tool of alternative wwPDB validation information, pdbx-validation v1.6.5, is available.
A cross conversion environment of multi dimensional NMR spectra, xyza2pipe v1.0.4, is available.
NMR-STAR Dictionary v3.2.1.18 is available.
NMR-STAR Dictionary v3.2.1.15 is available.
mmCIF-validation and mmCIF-validation-alt are available via either HTTP or rsync protocol. Note that these archives are experimental and may be changed or replaced in the future.
The article about NMR-STAR has been published in J. Biomol. NMR.
A generation tool of alternative wwPDB validation information, pdbx-validation v1.4.0, is available.
A database replication tool based on XML Schema, xsd2pgschema v3.0.8, is available.
NMR-STAR Dictionary v3.2.1.12 is available.
The article about PDB archive has been published in Nucleic Acids Res.
We made a presentation about PDBj-BMRB activities and alternative wwPDB validation reports at The day of TOGO 2018.
We made PDBj luncheon seminar about alternative wwPDB validation reports at The 56st Annual Meeting of the Biophysical Society.
BMRB/XML, BMRB/RDF, BMRB/JSON, and BMRB RDB Snapshot archives are based on the NMR-STAR Dictionary v3.2.1.9.
NMR-STAR Dictionary v3.2.1.9 is available.
NMR data analysis tool, MagRO-NMRView 2.01.15 released.
Launch web services enabling SSL.
A nmrML converter for BMRB metabolomics entries, BMSxNmrML v1.2.0, is available.
NMR data analysis tool, MagRO-NMRView 2.01.13, bug fixed version released.
Full-text index generator of OWL literal, owl-indexer v1.2.5, is available.
BMRB/XML, BMRB/RDF, BMRB/JSON and BMRB RDB Snapshot archives are based on the NMR-STAR Dictionary v3.2.1.5.
NMR-STAR Dictionary v3.2.1.5 is available.
PDBML-validation and wwPDB/RDF-validation are available via either HTTP or rsync protocol. Note that these archives are experimental and may be changed or replaced in the future.
NMR-STAR Dictionary v3.2.1.2 is available.
VirtualBox image (ova) file for MagRO-NMRView and Filt_Robot with CNN noise filter in NMRToolBOX has been updated.
NMR-STAR Dictionary v3.2.0.15 is available.
BMRB/XML, BMRB/RDF, BMRB/JSON and BMRB RDB Snapshot archives are based on the NMR-STAR Dictionary v3.2.0.15.
We have moved SCM site for the following software developped by PDBj-BMRB, BMRBxTool, BMRBoTool, and BMSxNmrML. The software is released under Apache Licence V2, respectively.
NMR-STAR Dictionary v3.2.0.13 is available.
BMRB/JSON archive is refreshed.
A nmrML converter for BMRB metabolomics entries, BMSxNmrML v1.1.0, is available. nmrML documents of the BMRB metabolomics entries are updated from v1.0.rc1 to v1.0.0.
Full-text index generator of OWL literal, owl-indexer v1.2.2, is available.
Quick instructions for CNN noise filter are available.
VirtualBox image (ova) file for MagRO-NMRView and Filt_Robot with CNN noise filter in NMRToolBOX has been restored.
BMRB RDB Snapshot is based on PostgreSQL 10's tool chain.
A quick tool for fully automated peak identification and noise filtration using Deep Neural Networks, Filt Robot, is available.
The article about nmrML has been published in Analytical Chemistry.
A cross conversion environment of multi dimensional NMR spectra, xyza2pipe v1.0.3, is available.
NMR data analysis tool, MagRO-NMRView 2.00.12, is available. New feature "Noise/Signal recognition by Deep Neural Networks" added.
BMRB/XML, BMRB/RDF, BMRB/JSON, and BMRB RDB Snapshot archives are based on the NMR-STAR Dictionary v3.2.0.11.
NMR-STAR Dictionary v3.2.0.11 is available.
The article about Data-out activity of PDBj-BMRB group has been published in Protein Science.
The article about NMRBox, A Resource for Biomolecular NMR Computation, has been published in Biophysical Journal.
Legacy ADIT-NMR deposition system has been retired. wwPDB news
Updated ADIT-NMR system will continue to accept NMR data associated with a structure currently not accepted by the wwPDB OneDep system (for example, relaxation data, and primary time-domain data) as well as experimental NMR data not associated with deposition of 3D coordinates (BMRB Only).
Legacy ADIT-NMR deposition system no longer accepts new session. Live sessions can be accessed until September 30th, 2016. Please use the wwPDB deposition system for new deposition. wwPDB news
The article about BMRB/XML, and BMRB/RDF has been published in Journal of Biomedical Semantics.
Validation reports for NMR and EM structures are now available. wwPDB news
wwPDB deposition system is now available for NMR and EM structures.