Genomics, Proteomics, Metabolomics, Structural Genomics, Structural Proteomics
BMRB Metabolomics database
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: 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.
TargetTrack, originally TargetDB, is a protein target and protocol registration
database that was developed and hosted at Rutgers University to register and track information for the NIH P50 funded
structural genomics centers. The database has since grown to include data contributed internationally and has merged
with the Proteing Expression database PepcDB into a single resource. It is funded by the US National Institutes of Health
(NIH) through its Protein Structure Initiative (PSI).
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.