darren cikaluk wrote:
>> I am going to be making a fusion protein from part the cDNA I have just
> cloned. I need to pick a region of my 800 aa protein-encoded cDNA but
> I'm not to sure where to choose. I know it should be the least
> hydrophobic etc. but does anyone know of a program that finds the most
> antigenic region of your protein? I know there is one out there but I
> forget the name.
Well, DNA Strider, GCG, MacVector, and DNAStar all have components which
will predict the antigenic index of protein sequences...and this is
based on hydrophilicity, surface probability, and flexibility. Also,
remember these algorithms are based on those proteins out there which
have actually been purified and crystallography studies performed on to
determine that they actually have these secondary structural elements.
If you use each of these predicitons (anitgenic index, hydrophilicity,
surface probability, and flexibility) to make your choice, then you
should have fair success. However, from personal experience, it can
still be a crap shoot....
Hope that helps in any small way.....