about bioinformatics                  

发信人: kingsyl (阅读文献中), 信区: Bioinformatics
标  题: about bioinformatics
发信站: 北大未名站 (2001年03月12日19:45:10 星期一), 站内信件

Bioinformatics has two main tasks in the Protein Structure Factory: To
predi
ct what can be done and to propose what should be done. Predicting what
can
be done is equivalent to identifying proteins that will permit their
three-d
imensional structures to be determined by X-ray crystallography or NMR
spect
roscopy. These proteins will have some properties in common. They will be
so
luble in aqueous buffers up to a critical concentration, they will have a
de
fined globular structure, and this structure will be stable for at least
as
long as it takes to grow and expose crystals or to measure the NMR
spectra.
Proteins that contain long stretches of hydrophobic or charged amino-acid
re
sidues, have extended sequence repeats or use a limited repertoire of
amino
acids over long polypeptide segments often do not display these
properties.
However, they may still contain single or multiple domains that permit
struc
ture analysis. In addition, bioinformatics will provide valuable
information
aiding the structure determination by predicting sites of
post-translationa
l modification and identifying proteins of known, similar tertiary
structure
. Structural prediction will be used to decide whether a given protein
will
be studied by NMR spectroscopy or by X-ray diffraction or, for the latter
ca
se, whether its structure analysis will require experimental phase
determina
tion or can be based on a homologous model.
To propose what should be done is the more challenging task. It is
equivalen
t to finding proteins with interesting properties such as novel folds or
a f
unction in biochemical pathways that may be associated with disease. The
mor
e interesting a protein appears, the more effort will have to be invested
in
its structure analysis. Computational tools for functional sequence
assignm
ents are currently being developed21. This work addresses questions
concerni
ng the subcellular localization of proteins, their membership in families
de
fined by function22-24 and their involvement in pathological states25

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