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Biological Magnetic Resonance Data Bank

Public depository that collects, annotates, archives, and disseminates important spectral and quantitative data derived from nuclear magnetic resonance (NMR) spectroscopic investigations of biological macromolecules and metabolites recognized by the International Society of Magnetic Resonance and by the IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. BMRB provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR. BMRB is a partner in the Worldwide Protein Data Bank. The BMRB archive consists of four main data depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors and derived data (relaxation parameters, residual dipolar couplings, hydrogen exchange rates, pK(a) values, etc.), (ii) databases for NMR restraints processed from original author depositions available from the Protein Data Bank, (iii) time-domain spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules and (iv) a database of one- and two-dimensional (1)H and (13)C one- and two-dimensional NMR spectra for over 250 metabolites. The BMRB website provides free access to all of these data. BMRB has tools for querying the archive and retrieving information and an ftp site where data in the archive can be downloaded in bulk. BMRB will accept: quantitative NMR data for a peptide, protein, nucleic acid, or polysaccharide and their ligands and cofactors assigned on an atom-specific basis, and data derived from the analysis of such data. Submitted data are to be in valid NMR-STAR format; they may be created by tools that output data in this format. The types of NMR data that can be included in a deposition and the mandatory supporting information accompanying a deposition are reviewed yearly by the BMRB Advisory Board. BMRB data is listed by: * Macromolecular types * NMR spectral parameters * Kinetics * Thermodynamics * Restraints * Small molecule structures * Time-domain sets * Solid-state NMR * Unfolded proteins * Binding Data * Diseases * NMR data combined with coordinates and restraints In collaboration with the Protein Data Bank (PDB, Rutgers University) and Nucleic Acid Data Bank (NDB, Rutgers University), BMRB aims to develop into the collection site for structural NMR data in proteins and nucleic acids. Steps are being taken at BMRB to achieve this capability, which will include transmission of all relevant data to the PDB and NDB collections. In addition, BMRB has the goal of archiving NMR-specific data including assigned chemical shifts, J-couplings, relaxation rates, and chemical information derived from NMR investigations (for example, hydrogen exchange rates and pKa values). In developing these collections BMRB intends to be responsive to the needs and priorities of the scientific community.

URL: http://www.bmrb.wisc.edu/

Resource ID: nif-0000-21058     Resource Type: Resource     Version: Latest Version

Keywords

biomolecular, chemical, chemical shift, chemistry, j-coupling, metabolite, protein structure, spectroscopy, structure, nuclear magnetic resonance spectroscopy, protein, peptide, nucleic acid, biomolecule, nuclear magnetic resonance, polysaccharide, ligand, cofactor, carbohydrate, time-domain spectral data, spectral resonance, visualization, metabolomics, time-domain, blast, data set, nmr pulse sequence, data analysis service, metabolite, macromolecule, spectrum analysis, magnetic resonance, thermodynamics, kinematics, disease, histochemistry, molecule

Funding Information

NLM, LM05799

Additional Resource Types

Data Repository, Database

Availability

Public, Acknowledgement requested, The community can contribute to this resource, Free

Publication Link

http://nar.oxfordjournals.org/content/36/suppl_1/D402.long

Related To

Worldwide Protein Data Bank, PDB, Nucleic Acid Database

Abbreviation

BMRB

Parent Organization

Synonyms

BioMagResBank, Biological Magnetic Resonance DataBank

Comment

Access: Open
Reuse: http://www.bmrb.wisc.edu/bmrb/about/citing.html
Start date: 1996
Type: Disciplinary
Deposit: Accepting data for deposit - http://www.bmrb.wisc.edu/deposit/
(info provided by re3data.org)

Listed By

DataCite, 3DVC, re3data.org

Supercategory

Resource

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am September 20, 2010

Originated From

SciCrunch

Changes from Previous Version

    No Changes

    Version 4

    Created 2 weeks ago by Christie Wang

    Version 3

    Created 3 weeks ago by Christie Wang

    Version 2

    Created 3 weeks ago by Christie Wang

    Version 1

    Created 5 years ago by Anonymous

    BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.

    • Markley JL
    • J. Biomol. NMR
    • 2008 18

    We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. All PDB depositions of structures based on NMR data must now be accompanied by experimental restraints. A scheme has been devised that allows depositors to specify a representative structure and to define residues within that structure found experimentally to be largely unstructured. The BMRB now accepts coordinate sets representing three-dimensional structural models based on experimental NMR data of molecules of biological interest that fall outside the guidelines of the Protein Data Bank (i.e., the molecule is a peptide with 23 or fewer residues, a polynucleotide with 3 or fewer residues, a polysaccharide with 3 or fewer sugar residues, or a natural product), provided that the coordinates are accompanied by representation of the covalent structure of the molecule (atom connectivity), assigned NMR chemical shifts, and the structural restraints used in generating model. The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems.

    BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank.

    • Doreleijers JF
    • J. Biomol. NMR
    • 2003 26

    Experimental constraints associated with NMR structures are available from the Protein Data Bank (PDB) in the form of "Magnetic Resonance" (MR) files. These files contain multiple types of data concatenated without boundary markers and are difficult to use for further research. Reported here are the results of a project initiated to annotate, archive, and disseminate these data to the research community from a searchable resource in a uniform format. The MR files from a set of 1410 NMR structures were analyzed and their original constituent data blocks annotated as to data type using a semi-automated protocol. A new software program called Wattos was then used to parse and archive the data in a relational database. From the total number of MR file blocks annotated as constraints, it proved possible to parse 84% (3337/3975). The constraint lists that were parsed correspond to three data types (2511 distance, 788 dihedral angle, and 38 residual dipolar couplings lists) from the three most popular software packages used in NMR structure determination: XPLOR/CNS (2520 lists), DISCOVER (412 lists), and DYANA/DIANA (405 lists). These constraints were then mapped to a developmental version of the BioMagResBank (BMRB) data model. A total of 31 data types originating from 16 programs have been classified, with the NOE distance constraint being the most commonly observed. The results serve as a model for the development of standards for NMR constraint deposition in computer-readable form. The constraints are updated regularly and are available from the BMRB web site (http://www.bmrb.wisc.edu).

    BioMagResBank.

    • Ulrich EL
    • Nucleic Acids Res.
    • 2008 15

    The BioMagResBank (BMRB: www.bmrb.wisc.edu) is a repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies of biological molecules. BMRB is a partner in the Worldwide Protein Data Bank (wwPDB). The BMRB archive consists of four main data depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors (assigned chemical shifts, coupling constants and peak lists) and derived data (relaxation parameters, residual dipolar couplings, hydrogen exchange rates, pK(a) values, etc.), (ii) databases for NMR restraints processed from original author depositions available from the Protein Data Bank, (iii) time-domain (raw) spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules and (iv) a database of one- and two-dimensional (1)H and (13)C one- and two-dimensional NMR spectra for over 250 metabolites. The BMRB website provides free access to all of these data. BMRB has tools for querying the archive and retrieving information and an ftp site (ftp.bmrb.wisc.edu) where data in the archive can be downloaded in bulk. Two BMRB mirror sites exist: one at the PDBj, Protein Research Institute, Osaka University, Osaka, Japan (bmrb.protein.osaka-u.ac.jp) and the other at CERM, University of Florence, Florence, Italy (bmrb.postgenomicnmr.net/). The site at Osaka also accepts and processes data depositions.