Antigenic Index in Peptidestructure

Maggie Kasten kasten1 at jeflin.tju.edu
Wed May 14 15:31:41 EST 1997

Greetings all,

I would like to get some help interpreting the output from the GCG
program, Peptidestructure. My local GCG guru has not used this program.

My goal is to get an idea of which regions of my protein might prove
antigenic for making antibodies. From the description, Peptidestructure
should provide me this type of information. When I examine the antigenic
index column in the resulting Peptidestructure file, I have a number
associated with each amino acid ranging from -0.6 to +1.7. Right now I'm
working on the assumption that a run of high positive numbers indicates
that stretch of amino acids might prove more highly antigenic than, say,
a run of negative numbers. 

My first question is, is this true? I tried looking up the cited
reference by Jameson & Wolf in Computer Applications in the Bioscience,
but my library's subscription to CABIOS doesn't go back to 1988. So I
can't easily use the paper to give me a better idea of how to interprete
my results. 

Assuming that my initial assumption is correct, I would also like to get
an idea from people who use this program of how long a run needs to be
to be considered significantly antigenic or un-antigenic. Does anyone
know whether this program is truly a good way to predict antigenicity?
Are there other programs (preferably freeware or shareware) that are
better? I have access to both PCs and Macs.

Thanks for any help you can give!

Maggie Kasten			Voice: 215-503-4614
Pathology Department		FAX:   215-923-9626
Thomas Jefferson University	Philadelphia, PA

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