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 <germuth@unbc.ca> 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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