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BMRB now provides access to Metabolomics data.
Introduction to "Omics"
The growing field called Metabolomics detects and quantifies the
low molecular weight molecules, known as metabolites (constituents of the
metabolome), produced by active, living cells under different conditions
and times in their life cycles. NMR is playing an important role in
metabolomics because of its ability to observe mixtures of small molecules
in living cells or in cell extracts.
Genomics is a science that attempts to describe a living organism
in terms of the sequence of its genome (its constituent genetic material).
Genomics uses the techniques of molecular biology and bioinformatics to analyze
the sequences attributed to structural genes, regulatory sequences, and even
noncoding sequences. Genomics is closely related to, and sometimes considered
a branch of, Genetics, which is the study of genes and heredity.
Proteomics focuses on identifying when and where proteins are
expressed in a cell so as to establish their physiological roles in an organism.
Structural Genomics is a worldwide effort aimed at determining the
three-dimensional structures of gene products in an efficient and high-throughput
mode. When the focus is on proteins, this effort may be called Structural
Proteomics. Whereas a structural biologist may work to thoroughly understand
the structure and function of one, or maybe a few proteins, structural genomics
efforts focus on determining the structures of large numbers of proteins without
prior regard to function. Several structural proteomics groups pursue the
structures of proteins that are "unique", generally ones that have less than 30%
sequence identity to a protein with a known structure in the Protein Data Bank.
The objective here is to enlarge our understanding of sequence-fold relationships
so that we are better able to predict structures from sequences. Other structural
proteomics centers have the goals of determining structures of all proteins from
a given organism or all structures of a particular class or family of proteins.
The Protein Data Bank (PDB) is the
international repository for biomolecular structure data. To find more information
about protein targets studied by structural genomics efforts, including the target
progress, protocols, structures, annotations, models, and DNA clones, visit the
PSI Structural Genomics
Knowledgebase.
TargetDBis a protein target registration
database that is hosted at Rutgers University and funded by the US National
Institutes of Health (NIH) through its Protein Structure Initiative
(PSI). It was originally
developed to register and track information for the NIH P50 funded structural genomics
centers, but has since grown to include data contributed internationally.
Why Structural Genomics is Important to the BMRB
Structural genomics efforts are producing a wealth of experimental data
from NMR studies that are linked to high-quality three-dimensional structures
of proteins. The "rules" of the international structural genomics effort mandate
that all data be deposited in a timely fashion. This includes coordinates of
three-dimensional structures deposited at PDB and for NMR structures, chemical
shifts, coupling constants, and other relevant data at BMRB. In addition, some
of the structural genomics centers are depositing the original NMR spectra as
time-domain data sets in BMRB. These data sets will allow structures to be
recalculated by others who may wish to practice their skills or test novel
methods for structure determination from NMR data. Data from structural genomics
centers are valuable to BMRB because they are enlarging the set of NMR parameters
and three-dimensional structures determined under comparable conditions.
NMR chemical shift data already are being used to determine secondary
structure in proteins and to set limits on a protein's conformation. As BMRB's
pool of assigned NMR data associated with structures increases, it will become
easier to determine structures of proteins from sparse data sets. These
data will be important for determining structures of larger proteins for
which it is difficult to obtain full data sets.
To make the pool of data most useful, it is important for the NMR community
as a whole to deposit their data and for these data to be in a standard, usable
format.
The mission of BMRB is to collect, archive and disseminate the quantitative
data derived from NMR spectroscopic investigations. The high throughput mode of
structural Genomics investigations means that those projects are major contributors
to BMRB. BMRB has developed standards for formatting and data definitions specified
for Structural Genomics.
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