Thanks to everyone who replied

Simon Andrews simon.andrews at
Mon May 8 07:09:36 EST 2000

Toby Skinner wrote:
> This is just a quick thanks to everyone who replied to my mail a few days
> ago, I realise it was a bit rash at places and I appologise if anyone found
> it a bit pushy.  Anyway, I have read the replies and the information is very
> useful, as it happens I have read a lot of approachs to protein folding but
> each one seems to be fairly different, I am using the Chou & Fasman rules,
> not because their particulary accurate but it was the easiest to understand
> (I am a Compuer Science & AI student after all).

The Chou and Fasman rules are a *very* simplified approach to the
problem of protein folding.  They have been superseded several times
since their creation.  They are also only predictors of secondary
strucutre, and will not relate this to tertiary structure.  

If you are using them  merely to make suggestions for conservative
mutations, then you could look at one of the standard PAM or BLOSUM
scoring matrices.  These are simply tabulated values which relate to the
frequency with which a given amino acid is observed to be substited with
all other amino acids in groups of homologous proteins.  This should
also be very easy to incorporate into a program.

> If you happen to have a bit of time then I would really appreciate it if you
> would be able to comment on the results of my program trying to generate a
> new (possibly) haemoglobin protein. I realise it will be inacurate but
> because I'm not a biochemist I wont realise exactly why it wont be perfect.

If you have something reasonally concise which describes exactly what
you have done then why not post it here?  I'm sure people would be happy
to comment on it.


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