Primary 2 Secondary folding rules

Frank Fuerst fant.1 at gmx.net
Thu Jan 27 06:41:14 EST 2000


Toby Skinner wrote:

> However I have little knowledge of proteins and the last time I talked
> about this with a biologist, he said that there was no point because
> the secondary structure of a protein is context sensitive such that you
> can only get about a 70% correct structure by looking only at the
> amino-acid sequence (and not at the spatial relationship between
> helices, beta sheets etc).

Right.

> If your this far then thankyou for sticking with me, what I need is a
> set of rules for predicting the secondary structure given the primary
> structure.  The idea being that an algorithm for predicting structures
> 70% correct is better than nothing, also I can then start on a new
> algorithm for applying a different set of rules for folding the
> secondary structure into the tertiary structure.
> 
> I understand that I am grossly simplifying this but I have spent a long
> time on this dissertation and I would really like to sort this problem
> out.

Are you familiar with other attempts on structure prediction? It
seems, not too well. 

I feel you should go a bit into biology and biologists' structure
prediction literature. For a starting point, try "CASP" in PubMed.

Frank
-- 
Potsdam University, Germany

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