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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.

Information

Mar 14, 2024

The article on validation of structural model in PDB using NMR restraints has been published in Structure.


Jun 25 - Jul 1, 2023

We attended BioHackathon 2023. The preprint of outcomes at the meeting has been published at BioHackrXive.

Jun 14, 2023

We are pleased to announce the release of corrected/combined NMR data files for existing NMR entries of the PDB Core Archive. wwPDB NEWS

Sep 6, 2023

A generation tool of alternative wwPDB validation information, pdbx-validation v4.4.29.

Jul 7, 2023

A database replication tool based on XML Schema, xsd2pgschema v4.4.7/5.3.7, is available.

Jan 6, 2023

The article about activities of BMRB/BMRBj groups has been published in Nucleic Acid Res.


Dec 19, 2022

A database replication tool based on XML Schema, xsd2pgschema v4.4.3/5.3.3, is available.

Dec 20, 2022

A generation tool of alternative wwPDB validation information, pdbx-validation v4.4.14.

Jan 11, 2022

A plot showing well-defined regions has been added to the content for combined NMR restraints.

Jan 8, 2022

The article about activities of BMRBj group has been published in Protein Science.


Oct 5, 2021

Incorporated AlphaFold Protein Structure Database sequence information as BLAST search results for each BMRB entry.

Sep 24, 2021

Tools for BMRB/XML and BMRB/RDF are update. The namespaces of BMRB/XML and BMRB/RDF will be changed respectively.

Sep 21, 2021

A nmrML converter for BMRB metabolomics entries, BMSxNmrML v1.3.0, is available.

Aug 18, 2021

Depositor can submit a release request for an On-Hold entry from the author view page by specifying PubMed ID of the primary citation.

Jul 30, 2021

Graphical content for the chemical shift validation reports is available.

Jul 29, 2021

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.

Jul 26, 2021

Depositor can access refreshed author view page for uploaded or processed data files. The page contains detailed validation information and graphically represented summary content.

Jul 13, 2021

RCI and derived parameters (S2, NMR RMSD) plots are added as graphical contents for the NMR combined restraints.

Apr 26, 2021

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.

Apr 21, 2021

Entries with extended PDB and CCD ID codes will be distributed in PDBx/mmCIF format only. wwPDB NEWS

Dec 28, 2021

A database replication tool based on XML Schema, xsd2pgschema v4.2.3/5.1.3, is available.

Jan 28, 2021

Revised statistics page on BMRB entries is accessible.

Jan 21, 2021

Graphical content for NMR combined restraints of PDB/BMRB entries is available.

Dec 17, 2021

A generation tool of alternative wwPDB validation information, pdbx-validation v4.4.4.


Dec 24, 2020

A database replication tool based on XML Schema, xsd2pgschema v5.0.0, is available, which requires JDK14 or later.

Dec 16, 2020

A generation tool of alternative wwPDB validation information, pdbx-validation v3.0.0, is available, which supports NMR restraint validation.

Nov 17, 2020

We released a JSON Schema for the combined NMR restraints report file, which contains restraint statistics and diagnostic information.

Oct 23, 2020

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.

Aug 31, 2020

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.

Aug 26, 2020

The first PDB entries, 7JIA and 7JIY deposited by the NMR unified data, have been released.

Nov 27, 2020

A generation tool of alternative wwPDB validation information, pdbx-validation v2.0.16, is available.

Jul 22, 2020

We have added content on emerging Coronavirus infectious disease (COVID-19) caused by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Nov 30, 2020

A database replication tool based on XML Schema, xsd2pgschema v4.1.4, is available.

May 4, 2020

OneDep began accepting upload of NMR experimental data as a single file, either in NMR-STAR or NEF format.

Feb 10, 2020

A generation tool of alternative wwPDB validation information, pdbx-validation v2.0.3, is available, which supports EM map/model validation.

Feb 1, 2020

The article about BMRB has been published in Method Mol. Biol.

Jan 15, 2020

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


Dec 25, 2019

A generation tool of alternative wwPDB validation information, pdbx-validation v2.0.1, is available, which supports EM map/model validation.

Dec 19, 2019

A database replication tool based on XML Schema, xsd2pgschema v4.0.5, is available.

Nov 19, 2019

A generation tool of alternative wwPDB validation information, pdbx-validation v1.6.5, is available.

Feb 28, 2019

A cross conversion environment of multi dimensional NMR spectra, xyza2pipe v1.0.4, is available.

Jan 25, 2019

NMR-STAR Dictionary v3.2.1.18 is available.

Jan 18, 2019

NMR-STAR Dictionary v3.2.1.15 is available.

Jan 15, 2019

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.


Dec 22, 2018

The article about NMR-STAR has been published in J. Biomol. NMR.

Dec 19, 2018

A generation tool of alternative wwPDB validation information, pdbx-validation v1.4.0, is available.

Dec 6, 2018

A database replication tool based on XML Schema, xsd2pgschema v3.0.8, is available.

Nov 19, 2018

NMR-STAR Dictionary v3.2.1.12 is available.

Oct 24, 2018

The article about PDB archive has been published in Nucleic Acids Res.

Oct 5, 2018

We made a presentation about PDBj-BMRB activities and alternative wwPDB validation reports at The day of TOGO 2018.

Sep 16, 2018

We made PDBj luncheon seminar about alternative wwPDB validation reports at The 56st Annual Meeting of the Biophysical Society.

Aug 31, 2018

BMRB/XML, BMRB/RDF, BMRB/JSON, and BMRB RDB Snapshot archives are based on the NMR-STAR Dictionary v3.2.1.9.

Aug 17, 2018

NMR-STAR Dictionary v3.2.1.9 is available.

Jul 20, 2018

NMR data analysis tool, MagRO-NMRView 2.01.15 released.

Jul 5, 2018

Launch web services enabling SSL.

Jun 29, 2018

A nmrML converter for BMRB metabolomics entries, BMSxNmrML v1.2.0, is available.

Jun 14, 2018

NMR data analysis tool, MagRO-NMRView 2.01.13, bug fixed version released.

Jun 9, 2018

Full-text index generator of OWL literal, owl-indexer v1.2.5, is available.

Apr 17, 2018

BMRB/XML, BMRB/RDF, BMRB/JSON and BMRB RDB Snapshot archives are based on the NMR-STAR Dictionary v3.2.1.5.

Apr 13, 2018

NMR-STAR Dictionary v3.2.1.5 is available.

Apr 9, 2018

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.

Apr 5, 2018

NMR-STAR Dictionary v3.2.1.2 is available.

Mar 29, 2018

VirtualBox image (ova) file for MagRO-NMRView and Filt_Robot with CNN noise filter in NMRToolBOX has been updated.

Feb 5, 2018

NMR-STAR Dictionary v3.2.0.15 is available.

Feb 9, 2018

BMRB/XML, BMRB/RDF, BMRB/JSON and BMRB RDB Snapshot archives are based on the NMR-STAR Dictionary v3.2.0.15.

Feb 7, 2018

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.

Jan 24, 2018

NMR-STAR Dictionary v3.2.0.13 is available.

Jan 24, 2018

BMRB/JSON archive is refreshed.


Dec 20, 2017

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.

Dec 4, 2017

Full-text index generator of OWL literal, owl-indexer v1.2.2, is available.

Nov 22, 2017

Quick instructions for CNN noise filter are available.

Nov 22, 2017

VirtualBox image (ova) file for MagRO-NMRView and Filt_Robot with CNN noise filter in NMRToolBOX has been restored.

Nov 8, 2017

BMRB RDB Snapshot is based on PostgreSQL 10's tool chain.

Oct 19, 2017

A quick tool for fully automated peak identification and noise filtration using Deep Neural Networks, Filt Robot, is available.

Oct 16, 2017

The article about nmrML has been published in Analytical Chemistry.

Oct 12, 2017

A cross conversion environment of multi dimensional NMR spectra, xyza2pipe v1.0.3, is available.

Oct 11, 2017

NMR data analysis tool, MagRO-NMRView 2.00.12, is available. New feature "Noise/Signal recognition by Deep Neural Networks" added.

Oct 10, 2017

BMRB/XML, BMRB/RDF, BMRB/JSON, and BMRB RDB Snapshot archives are based on the NMR-STAR Dictionary v3.2.0.11.

Sep 26, 2017

NMR-STAR Dictionary v3.2.0.11 is available.

Sep 18, 2017

The article about Data-out activity of PDBj-BMRB group has been published in Protein Science.

Apr 25, 2017

The article about NMRBox, A Resource for Biomolecular NMR Computation, has been published in Biophysical Journal.

Mar 7, 2017

The article about OneDep has been published in Structure.


Oct 1, 2016

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).

May 31, 2016

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

May 5, 2016

The article about BMRB/XML, and BMRB/RDF has been published in Journal of Biomedical Semantics.

Mar 7, 2016

Validation reports for NMR and EM structures are now available. wwPDB news

Feb 1, 2016

wwPDB deposition system is now available for NMR and EM structures.