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The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) is an
open access Open access (OA) is a set of principles and a range of practices through which research outputs are distributed online, free of access charges or other barriers. With open access strictly defined (according to the 2001 definition), or libre op ...
repository of
nuclear magnetic resonance Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a ...
(NMR) spectroscopic data from
peptides Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A p ...
,
proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
,
nucleic acids Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main clas ...
and other biologically relevant molecules. The database is operated by the
University of Wisconsin–Madison The University of Wisconsin–Madison (University of Wisconsin, Wisconsin, UW, UW–Madison, or simply Madison) is a public land-grant research university in Madison, Wisconsin. Founded when Wisconsin achieved statehood in 1848, UW–Madison ...
and is supported by the
National Library of Medicine The United States National Library of Medicine (NLM), operated by the United States federal government, is the world's largest medical library. Located in Bethesda, Maryland, the NLM is an institute within the National Institutes of Health. Its ...
. The BMRB is part of the Research Collaboratory for Structural Bioinformatics and, since 2006, it is a partner in the
Worldwide Protein Data Bank The Worldwide Protein Data Bank, wwPDB, is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly availa ...
(wwPDB). The repository accepts NMR spectral data from laboratories around the world and, once the data is validated, it is available online at the BMRB website. The database has also an ftp site, where data can be downloaded in the bulk. The BMRB has two mirror sites, one at the Protein Database Japan (PDBj) at
Osaka University , abbreviated as , is a public research university located in Osaka Prefecture, Japan. It is one of Japan's former Imperial Universities and a Designated National University listed as a "Top Type" university in the Top Global University Project. ...
and one at the Magnetic Resonance Research Center (CERM) at the
University of Florence The University of Florence (Italian: ''Università degli Studi di Firenze'', UniFI) is an Italian public research university located in Florence, Italy. It comprises 12 schools and has around 50,000 students enrolled. History The first universi ...
in Italy. The site at Japan accepts and processes data depositions.


Content


NMR spectral values and derived information

The bulk of the data deposited at the BMRB consists of over 11,900 entries containing 1H, 13C, 15N and 31P assigned chemical shifts and
coupling constants In physics, a coupling constant or gauge coupling parameter (or, more simply, a coupling), is a number that determines the strength of the force exerted in an interaction. Originally, the coupling constant related the force acting between tw ...
of peptides, proteins and nucleic acids. Other derived data like residual dipolar couplings (RDC), relaxation parameters, NOE values, order parameters and hydrogen exchange rates are also available. The database contains also a smaller amount of NMR data from carbohydrates, cofactors and ligands. These data are crossreferenced to 3D structures in the PDB when available. The NMR data are provided in the NMR-STAR file format and a number of format conversion tools are available at the site to convert files from NMR-STAR to other formats.


NMR restraints grid

The NMR restraints grid contains NMR restraints data from over 2500 proteins and nucleic acids collected from PDB depositions. The grid is constructed as four subsets of data: *The original NMR data: This subset contains data as found in depositions from the PDB. The data are in various different file formats and contain information about interatomic distances,
dihedral angles A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the uni ...
and RDC restraints. *Parsed restraints data: Most of the entries in the original data subset have been parsed into the NMR-star file format facilitating its access and use. This subset contains over 9,400 entries. *Converted restraints data (DOCR): Over 500 entries in the parsed subset have been converted to make the atom nomenclature consistent with the corresponding atomic coordinates. *Filtered restraints data (FRED): The data in the DOCR were filtered to remove duplicates, redundancies, inconsistencies and values that do not contribute to structure calculations.


Time-domain data

The BMRB has archived sets of raw time-domain data collected from NMR experiments carried out to calculate restraints and chemical shifts in peptides, proteins and nucleic acids. This collection contains over 200 entries and in many cases the pulse-sequences and the acquisition parameters used are also available.


NMR spectral data from metabolomic compounds

The BMRB hosts a database containing NMR spectral data from hundreds of metabolomic compounds. For most compounds, 1H NMR, 13C NMR, 13C 90o DEPT, 13C 135o DEPT, 1H-1H TOCSY and 1H-13C
HSQC The heteronuclear single quantum coherence or heteronuclear single quantum correlation experiment, normally abbreviated as HSQC, is used frequently in NMR spectroscopy of organic molecules and is of particular significance in the field of protein NM ...
are available.


NMR statistics

The BMRB provides a collection of NMR statistical data, including chemical shift distributions for individual atoms in
amino acids Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
,
ribonucleotides In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. Ribonucleotides themselves are basic mo ...
and
deoxyribonucleotides A deoxyribonucleotide is a nucleotide that contains deoxyribose. They are the monomeric units of the informational biopolymer, deoxyribonucleic acid ( DNA). Each deoxyribonucleotide comprises three parts: a deoxyribose sugar ( monosaccharide), a n ...
. The data are presented as interactive histograms and density plots.


Searches


The BMRB query Grid Interface

The BMRB Query Grid Interface, allows to search the database by molecule type (peptide, protein, DNA,
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
, etc.), by data type (1H chemical shift, 13C chemical shift, coupling constant, etc.), by PDB ID number and by BMRB accession number.


FASTA search

The BMRB site also contains a
FASTA FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program ...
search page where the database can be searched for matching nucleotide or peptide sequences.


Search Archive page

From the Search Archive page, it is possible to carry out searches by accession number, author, title, molecule name, and by ID number from other common databases. An Advanced Search option allows to carry out queries using a variety of search parameters like: entry information, citations, molecular assembly, experimental descriptions, NMR parameters, etc. The page contains also links to restraints and metabolomics searches


Restraints search

The NMR restraints grid can be searched by PDB or BMRB number, and also by specific kinds of restraints, like torsion angle, distance, residual dipolar coupling, etc.


Metabolomics search

Through the metabolomics search page. the database can be searched for specific compounds by name, molecular formula, molecular weight, ID number and molecular structure. It can be searched for entries with specific experimental conditions (solvent or field strength). The interface allows also to search for compounds with matching 1D or 2D NMR spectral peak lists.


Data deposition

The BMRB accepts depositions from research groups around the world. Deposition of data containing only NMR spectral data (with no coordinates data) is carried out through the BMRB site using the ADIT-NMR deposition system. The types of data accepted include: NMR spectral parameters, relaxation data, and kinetic and thermodynamic data. Data must be entered in the NMR-STAR format, conversion from other common formats can be carried out using the STARch file converter provided at the site. The site also contains an NMR-STAR template generator which produces formatted tables where NMR data can be entered. NMR time-domain data is uploaded separately via ftp. The BMRB encourages depositors to validate their NMR data before deposition, using one of the validation tools available at the BMRB site, to check for inconsistencies and errors. . Once the data is deposited, it is checked for completeness, consistency and annotated, links to other databases are added and a BMRB accession number is generated. Deposition of data containing NMR and coordinates data is done through the OneDep deposition system of the wwPDB. Once the data is validated and accepted, it receives PDB and BMRB accession numbers.


References


External links


Biological Magnetic Resonance Data Bank websiteWorldwide Protein Data Bank website
{{University of Wisconsin–Madison, state=collapsed Biological databases Public domain databases Online databases United States National Library of Medicine University of Wisconsin–Madison