I would say this goes far beyond the capability of Jmol. You will need way
more sophisticated tools to do those "adjustments"
On Thu, Apr 25, 2013 at 7:27 PM, Aaron Germuth <[email protected]> wrote:
> > I'm interested in your project and will be happy to collaborate with you.
>
> Since I'm doing this project through my University, I'm not sure if I'm
> legally allowed to let you help with the physical code portion. I'll have
> to get back to you. However, If this is allowed, I would gladly embrace
> your help.
>
> > what is exactly the "HP protein folding model" ?
>
> The HP Protein Folding Model is a simplified model which computers can use
> to fold proteins. Computationally, folding proteins is a very expensive
> process. Even with the massive simplification that there are only two
> different types of amino acids the process still takes an unreasonable
> amount of time for large proteins. And this isn't even considering hydrogen
> bonds or ionic interactions.
> Anyway, in the model, we turn each amino acid into either a hydrophobic or
> hydrophilic amino acid, and allow a genetic algorithm to attempt to put
> hydrophobic amino acids on the inside, and hydrophilic amino acids on the
> outside. The resulting polypeptide is our folded protein.
> This has a little bit more information "
> http://en.wikipedia.org/wiki/Hydrophobic-polar_protein_folding_model";
>
> > the amino acid residues will not necessarily fit in those "cells"
>
> This is a problem I've thought about, as some amino acids such as
> phenylalanine are much larger than say, glycine. The goal I'm personally
> going for is to get as close as we can to the folded model, while obeying
> molecular structure. We might have to edit the Jmol structure if overlap
> occurs.
>
> > a realistic polypeptide backbone will not match the 90 degree angles.
>
> This goes as before. We can attempt to rotate the peptide bond as much as
> possible to get the closest match.
>
> > it is arguable whether inserting the structure of each amino acid
> residue into it is meaningful.
>
> The results given from the finished project also are not expected to give
> entirely realistic proteins. However, the results we do obtain can be
> directly compared to an experimentally found .pdb of proteins. This allows
> a direct comparison between computer generated results and the actual
> protein. To evaluate the results of the algorithm before, we simply had to
> observe that hydrophobic residues appeared in the middle, and hydrophilic
> residues on the outside.
>
> If you have any other questions I'd be happy to answer them.
>
> Aaron Germuth
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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