Computer-generated vaccines

Tue Nov 23 11:23:54 EST 1999

To adequately harness the power of computers in generating peptide vaccine
candidate sites, a physical chemical analysis of the interactions of
peptides and antibodies at a more basic, physical level than amino
acid combinatorics per se, needs to be addressed. 

For our, perhaps more atomic than molecular answer to this problem please

Kokolus, et. al,  Does the Fountain Epitope Model's Rhythmic Hydropathy
Continuum Pattern Satisfy the Requirements of a Nucleic Acid Meta-code or
Protein Meta-form?,  Ann. N.Y. Acad. Sci. 870:423-427.

Happy Thanksgiving, everybody!

William J. Kokolus, Ph.D.
President, Fountain's Rainbow Biomedicine,
Kenmore, New York

On Mon, 22 Nov 1999,
Tracy P. Hamilton wrote:

> Pierre wrote in message <818dle$2jee$1 at>...
> >What is the role of contingency/probability in protein folding ? If one
> >chain has many possible foldings, each affected with a given probability
> >amongst the population of molecules (like in evolution/population
> genetics),
> >is it possible to calculate all the variations ?
> [snip my previous post]
> One would not be able to go thorough all possible protein conformations.
> I *believe* (I am no protein folding expert, but a theoretician in a more
> fundamental sense) that current approaches are more empirical.
> Predict secondary structure (alpha helix, beta sheet, random coil) from
> part of the amino acid sequence, tertiary structure (overall shape) is from
> a different database, but similarly empirical.  Both are correct about half
> the time now, last I heard.
> A group was able to predict the sequence of a protein that would be
> the same shape as one of the zinc finger proteins, except without zinc!
> Makes one wonder why zinc fingers have zinc...
> Theory does currently play a large role in constraining structures,
> particularly
> NMR ones (solution structures based on H-H distances).  I don't have a
> good feel for what would happen if you applied one of the good protein
> force fields to the superoxide dismutase enzyme (or the mutant that
> has been identified with inherited ALS which has a more exposed
> active site).
> If I were to model the active site, I would probably put some geometric
> constraints on the active site to keep it in the neighborhood for at least
> some calculations.
> Tracy P. Hamilton

William Joseph Kokolus, Ph. D.
President, Fountain's Rainbow Biomedicine
69 Ferndale Ave.
Kenmore, N. Y. 14217-1003
phone and fax: (716) 873-6940
e-mail: cm006 at

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