BioMagResBank

Abstract

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, pKa 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 1H and 13C 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.

The Protein Data Bank archive as an open data resource

“…The wwPDB partners (RCSB PDB [15]; Protein Data Bank in Europe, PDBe [18]; Protein Data Bank Japan, PDBj [19]) developed clear guidelines and policies for data deposition and annotation. In 2006, the BioMagResBank (BMRB) archive of NMR experimental data joined the wwPDB [20,21]. An Advisory Committee consisting of international leaders in structural biology meets annually to review the activities and policies of the wwPDB.…”

NMR-based pharmacometabonomics: A new paradigm for personalised or precision medicine

“…The structure elucidation of novel metabolites requires the high standards associated with the identification of novel natural products [34] or novel drug degradation products [35] and would normally involve either: (i) the isolation and purification of the metabolite from the biological matrix and its full molecular structure characterisation by the standard array of methods including UV, IR, MS and NMR, or X-ray crystallography, or (ii) the synthesis of an authentic reference standard of the metabolite for comparison of its spectral properties with those of the same metabolite in the biological matrix. This novel structure elucidation work can be clearly differentiated from the second type of identification problem, that of structure confirmation of known metabolites, for which spectroscopic data is available in databases such as the Human Metabolite Database (HMDB) [36], the BioMagResBank (BMRB) [37] and COLMAR. [38] The key question for this structure confirmation work is what confidence the investigator has in the identification of the known metabolites.…”

Non invasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches

“…The HSQC TOCSY spectra were acquired as 1024 (F2) and 256 (F1) data points with 180 scans and an interscan delay of 1 s with 16 dummy scans. The NMR spectra were processed using Bruker TopSpin software (Bruker BioSpin GmbH) and assigned using the SpinAssign program at the PRIMe website (http://prime.psc.riken.jp/) (Akiyama et al 2008;Chikayama et al 2010;Chikayama et al 2008) and the Biological Magnetic Resonance Bank (http://www.bmrb.wisc.edu/metabolomics/query_metab.php) (Ulrich et al 2008). …”