Re: [Jmol-users] Help With Project Direction
> I realize what the basis and limitations are. Is this "HP" an > algorithm you have developed, is it published? No I certainly didn't develop it. HP Protein folding has been around in the literature for a while. Some examples below: Bui, T.; Sundarraj, G.; An Efficient Genetic Algorithm for Predicting Protein Tertiary Structures in the 2D HP Model. Genetic and Evolutionary Computation Conference. 385-392. 2005. Hoque, M.; Chetty, M.; Sattar, A.; Protein Folding Prediction in 3D FCC HP Lattice Model Using Genetic Algorithm. IEEE Congress on Evolutionary Computation. 2007. > I would say this goes far beyond the capability of Jmol. You will need way > more sophisticated tools to do those "adjustments" > More than whether Jmol is capable or not, my increasing concern is > whether this makes sense. > Not only overlap, but unrealistic bonding distances. I'm not sure > this is sensible. > You see? Speaking of rotating the bonds as much as possible is scary. > Peptide bonds do have their preferred orientations. > Not necessarily; too many constraints in the approximation. I'm not > sure any comparison can be made. > Anyway, I wish you good luck, but I'd say think it twice before > embarking into this. I'm beginning to feel this project may be too ambitious. Is there some other 3D visualization tool you know of, which does have such capability? Aside from difficulty, do you feel this is a worthy endeavour? I'm starting to worry that even if I did obtain molecularly 'valid' structures, they would be so different from the folded hp model that most meaning would be lost. Please don't be afraid to post your opinion, I'd rather figure out now than months into this. Thanks, Aaron Germuth -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help With Project Direction
> 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 -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help With Project Direction
The user enters in a sequence of h's and p's, which starts off as a linear chain of amino acids. After folding, the linear chain usually takes on a 'globular' form. Each amino acid is represented as a single red (hydrophobic) or blue (hydrophilic) sphere. The folding model does not deal with anything at the level of atoms, only amino acids. I hope this answers your question. Aaron Germuth This sounds very interesting. When you do the folding, do you do it strictly in terms of residue locations in space? That is, no real atoms? Or is there at least a backbone to work with? I'm not sure what you mean by minimization. Keep in mind this program is just an educational model and is not meant for proteins thousands of amino acids long. In fact, attempting to fold a protein even one hundred amino acids long would take over a day. I intend to use this only on very small proteins. Aaron Germuth - It seems to me there will be a significant amount of minimization to be done. That is beyond the scope of Jmol. Jmol can minimize small sections of a model, but not a full protein. -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Help With Project Direction
Greetings, Previously I have created a program which takes a sequence of hydrophobic or hydrophilic amino acids and folds it based of the HP protein folding model. The folded coordinates are given and displayed in a x-y-z grid format (as in an amino acid can only be located on integer x, y, z coordinates; no decimals). A typical folded protein resembles this: http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg What I hoping to add is to use Jmol to display this protein. However, instead of simply a ball representing the amino acid, I would like to show each molecule of each amino acid. My current idea of how I would go about this is as such: - Read in a real protein sequence ( Lys - Asp - Arg - etc ), and turn this into a string of hydrophobic or hydrophilic amino acids for my program to fold. - Once folded, replace each amino acid with it's actual molecules in Jmol, to do this I might - programmatically create a .pdb file for Jmol to read. To do this I would already have pdb files for all 20 amino acids stored, and displace their atoms to the grid coordinate given from the existing program. However, I would have to get the amino acids to be bonded together through peptide bonds, which seems tricky. Before I step into this large project, I would just like to ensure I'm on the right path and doing things the best/easiest way possible. I am quite new to Jmol and would very much appreciate any suggestions or things to look out for. If you have any questions, I am more than happy to answer them. Thank you for your time Aaron -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
