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Protein structure from scratch?

Douglas C Pearson dopearso at magnus.acs.ohio-state.edu
Tue Aug 9 10:38:45 EST 1994

In article <170097098S86.FJVAND00 at ukcc.uky.edu>,
Frank van de Loo <FJVAND00 at ukcc.uky.edu> wrote:
>Dear Modelers,
>This may be laughable, but I need to know.  Can one construct a model protein
>structure from scratch?  If one has a protein of a few hundred amino acids
>length and various types of data (homology, site-directed mutagenesis,
>photolabelling, etc), and can come up with a hypothetical super-secondary or
>tertiary structure on paper for most or part of it, is it possible to constuct
>the model in a program that can then display it and be used for further

not to continue to bang on a dead horse, since i'm about the seventh person to
respond here, but it's possible.  don't count on earth-shattering accuracy,
but you can get a fairly decent educated guess.  somebody mentioned earlier up
to a 65% accurate model, i think...i'd say that's a reasonable number.  we're
planning on using quanta in our lab to build some homology models of a few
proteins we want to do elecrostatic analysis on.  it will be interesting to see
how that turns out.

>            I have been trying to do this in Hyperchem, with much frustration
>since I can't fold the polypeptide about very well once I've made it.  Is
>there a way, or am I just trying to do something impossible?  All advice
>greatly appreciated!

now, if you're using hyperchem, i'd say give up before you strain your brain
cells.  8-)  there is much better software around for doing this kind of thing
...stuff like quanta will serve your needs very nicely.  quanta doesn't come
cheap, though.

>Frank van de Loo
>USDA/ARS, University of Kentucky.

to steer this thread in a new direction, what would you guys say the most
important details in building a protein structure based on homology are?
mr (dr?) van de loo mentioned mutagenesis and photolabeling as well.  how much
more reliable is that kind of data compared to homology data?  are there any
other things that somebody wanting to do this kind of thing should look out

all contributions greatly appreciated...

"clueless chuck" aka douglas c pearson jr -- dopearso at magnus.acs.ohio-state.edu
osu biophysics program -- bio113 teaching assistant at large -- married 1 year!

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