Modeling Structure By Homology

Ram Samudrala ram at mbisgi.umd.edu
Fri Jul 5 18:09:39 EST 1996


Douglas Easton (dpeaston at Microagewny.com) wrote:

>I am currently modeling the structue of a protein using an X-ray
>structure for a protein, distantly homologous in sequence and in
>function. I am predicting the secondary structure using ssp, nnsp, GOR
>etc. And alligning sequence homologies and the real and predicted
>secondary structures. The results seem neat but my confidence in the
>approach is a bit shakey.

If it's really distant (how distant is it?), then you're on shaky
ground but I am not sure why you're doing this.  Is your goal only to
predict the secondary structure?  If so, I doubt any secondary
structure prediction method would be better in general than simply
taking the secondary structure assignment of the homolog according to
a good alignment.

For distant homologs, this is a good thing to do in order to confirm
your alignment.  I'd use PHD for predicting strucures also.

>Can you carry this analysis to the tertiary structure level?

Yes, that's what homology modelling is about.  I recommend looking at
the November 1995 issue of Proteins: Structure, Function, and Genetics
for some ideas on how to go about doing this, and the pitfalls
involved.

--Ram

me at ram.org  ||  http://www.ram.org  ||  http://www.twisted-helices.com/th
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