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, 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.

Figure 1.

DEVise interactive data visualization for data from BMRB entry 5991 [(39); BMRB accession code 5991] with a model from PDB entry 1R36 [(39); PDB accession code 1R36]. In the figure, the kinds of data that can be plotted are listed on the left, with the ‘HA delta chem shift’ selected, and the plot shown at the bottom of the visualization. A stretch of strong positive delta chemical shift values (indicative of a β-strand) is selected by placing the box around the values in the bar graph plot. These values are highlighted in green, and the corresponding residues are colored in green in the ribbon diagram of the PDB model (rendered using Jmol) present at the center of the visualization. The selected residues are highlighted in the window that displays the protein sequence.

Figure 2.

Summary page for the metabolite N-acetyl-l-glutamine from the BMRB metabolomics website.