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发信人: ray (大笨蛋), 信区: Biology
标 题: Re: a bioinformatics question
发信站: Unknown Space - 未名空间 (Mon Jun 14 10:54:42 2004) WWW-POST
I think it depends on the function of the protein. Some functions can be
easily predicted with its structure. For example, if it bind to some samll
ligands, then there should be a binding pocket. Or if binds with DNA/RNA(?),
then there should be highly charged part on the surface.. Protein-potein
binding sites are more difficult to be predicted.
There should be other info. to be used. If you get a protein structure right,
you have to assume a lot of things already. Such as if it's a membrane protein
or soluable protein? What's the PH enviroments, etc. Otherwise, you can't get
the right energy. ENVIROMENT, is important. A protein's function is not only
decided by itself, but also its enviroment, such as what moleculars it may
interact with. Right?
A structure may tell us the potein's potential function. We need to know its
enviroments to know what it exactly do.... I think that's the beginning of
system biology :)
【 在 lyms (davido) 的大作中提到: 】
: The three-dimensional structure of this protein can be predicted. However,
: there is no structure homology of this new protein in the protein database.
: How to predict the location of functional sitws? Thanks
:
:
:
: 【 在 wowotou (wowotou) 的大作中提到: 】
: : agree. there are two questios in the original post: protein structure
: : prediction and function/active site prediction. IMHO, the former is a lot
: : harder. Once the protein structure can be reliably predicted, the active
: site
: : can be predicted based upon sequence/structure homology, since they are
: : usually very conserved as the result of evolution.
: : 【 在 nohate (无恨) 的大作中提到: 】
: : :
: : : functional sites usually contain highly conserved residues and may have
: : : certain shape, if prediction can really work, finding the functional
site
: : : should be easy. But...
: : :
: : :
:
:
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※ 修改:·ray 於 Jun 14 10:54:42 修改本文·[FROM: 136.165.]
※ 来源:．Unknown Space - 未名空间 mitbbs.com．[FROM: 136.165.]
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