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Primary 2 Secondary folding rules

Toby Skinner tobyski at cogs.susx.ac.uk
Wed Jan 26 12:38:41 EST 2000


I'm a 3rd year student studying Computer Science & Artificial
Intelligence, I am currently attempting to build my dissertation but I
seem to have become stuck at a fairly important stage, any help would be
gratefully appreciated.

I am attempting to write an algorithm which takes the secondary
structure of a protein and returns a list of amino-acid sequences which
fold into the specified secondary structure (Inverse Folding Problem I
think it's called).

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).

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

Again, any help would be really appreciated.

Toby Skinner

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