BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules 		Member of WWPDB

BioMagResBank News

April 7, 2020

Plan to discontinue legacy formats and platforms

NMR-STAR v2.1 support will be discontinued

BMRB announces that the NMR-STAR v2.1 format will no longer be supported by BMRB after September 1, 2020. This will mean that all data from BMRB will be available in NMR-STAR versions 3.1 or higher. BMRB has been providing data in NMR-STAR v3.1 format for over ten years, and if you are not sure which version you are using, it is likely that you are already using v3.1 and that this change will not affect you. Users that need to convert older files to the new format, as well as developers whose software reads and/or writes NMR-STAR v2.1 files are invited to contact our help desk at [email protected] for help and orientation on updating files and/or support for the new format. The NMR-STAR format has evolved over the years, with the current format having improved data organization, enhanced metadata support, expanded data content, and enriched inter-operation with closely related data resources like the wwPDB, of which BMRB is a Core Archive for NMR experimental data.

ADIT-NMR deposition tool to be discontinued

BMRB announces the planned discontinuation of the ADIT-NMR deposition system. Depositors with open depositions started on ADIT-NMR should finish them by September 1, 2020. ADIT-NMR will no longer allow new depositions to be started beginning June 1, 2020. Depositors are encouraged to start new depositions using BMRBdep.

BMRBdep provides a streamlined, more responsive deposition experience, as well as better support for depositors, with a familiar but cleaner interface. Please contact BMRB’s help desk at [email protected] if you envision any problems with an open deposition due to this timeline.

December 1st, 2016

RBMRB 2.0 released

RBMRB version 2.0 has been released. RBMRB is a library in R which enables easy access of BMRB data in R environment. This version of RBMRB library is now available through CRAN archive. The developmental version is available at BMRB GitHub repository. Several new features like simulation of HSQC and TOCSY spectra and interactive chemical shift correlation plots have been added to version 2.0. Users may submit feature request or report any bugs through our GitHub repository. More information is available here

August 26, 2016

BMRB GitHub organization created

The BioMagResBank has created an organizational GitHub page and has moved the development of several of its tools there. You can access the page here.

BMRB Python NMR-STAR library released

A Python module for reading, writing, modifying, and validating NMR-STAR format files is now available for public use. This module makes it easy to interact with NMR-STAR files in Python by automatically handling all of the STAR syntax issues for you and much more. Features of the library:

  • Ability to load files directly from BMRB database or from disk.
  • Ability to validate files against the BMRB schema.
  • Object-oriented data model allows you to parse once and then read or modify the file in memory.
  • An optional C extension to make reading NMR-STAR files lightning fast.
  • A SANS parser mode is provided if you are currently using the python SANS parser and want to upgrade.
  • Read-only support for NMR-STAR version 2 files.
More information and documentation is available at the GitHub repository.

August 15, 2016

BMRB API and R library

A hybrid REST/JSON-RPC API to use for querying against the BMRB database is now available for public use. Most data in the macromolecule and metabolomics databases are accessible through the API. This API is free to use and doesn't require an API key. More information is available at the GitHub repository (https://github.com/uwbmrb/BMRB-API)

As an application of this API and to facilitate BMRB data analysis on the famous data analysis package R, a library is now available from BMRB GitHub repository (https://github.com/uwbmrb/RBMRB). With the help of this R library, user can now access BMRB chemical shift data directly in their R environment. More information is available on the GitHub documentation page.

August 5, 2016

wwPDB Validation Server Upgrade

The new wwPDB Validation Server at https://validate.wwpdb.org now generates preliminary validation reports for structures solved by NMR and 3D Electron Microscopy, in addition to X-ray crystallography.

wwPDB strongly encourages the use of the Validation Server at any time during the structure determination process, but particularly when preparing structures for deposition to the wwPDB. Validation Server reports provide identical information to the ones generated at deposition.

Structural models may be assessed independently or together with experimental data (crystallographic structure factors or NMR chemical shifts) for validation of model/data correspondence.

April 4th, 2016

AutoDep, ADIT-NMR, EMDep Deposition Systems to Be Retired, Effective September 30th 2016

In January 2014, the wwPDB launched a unified deposition, annotation, and validation system (RCSB PDB | PDBe | PDBj) for structures determined using X-ray crystallography. More than 14000 structures have been deposited, annotated, and validated using this system, with more than 9000 structures already released into the PDB archive. The new system uses the PDBx/mmCIF data format, which produces more uniform data, supports replacement of data files pre- and post-deposition, enhances communication with depositors, enables improved annotation, and provides validation reports based on recommendations from wwPDB expert task forces. Improvements to this system are regularly incorporated in response to user feedback. Detailed information and video tutorials are available.

An extended version of the unified wwPDB deposition, annotation, and validation system supporting structures determined by X-ray crystallography, NMR, and 3D EM was launched January 8th 2016. The extended system is integrated with the repositories for NMR and 3D EM experimental data and can assign both BMRB and EMDB accession codes.

Starting May 31st 2016, the legacy deposition systems, AutoDep, ADIT-NMR (BMRB|PDBj) and EMDep, will no longer accept new PDB and EMDB submissions. Depositors with in-progress sessions on the legacy systems will be able to access and complete their deposition sessions until September 30th 2016.

An updated ADIT-NMR system (available from BMRB and PDBj-BMRB) will continue to accept NMR data associated with a structure currently not accepted by the unified wwPDB deposition system (for example, relaxation data, and primary time-domain spectra) as well as experimental NMR data not associated with the deposition of 3D coordinates.

Questions and comments should be sent to [email protected].