\"Do it yourself\" Protein Design

Message boards : Rosetta@home Science : \"Do it yourself\" Protein Design

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Avi

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Message 23732 - Posted: 20 Aug 2006, 15:12:26 UTC

Not sure how logn this would take, but it sounds pretty cool. Let users get a hands-on understanding of the energy by displaying the one protein on the whole screen and letting the user manipulate each turn and watch the energy.
Maybe for the scientist a real-time energy calculation might help solidify theories on how the shapes affect the energy and/or make new thories.

p.s. any quick links somewhere to how the enrgy used is calculated? Something a lay-person can understand ;)
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Message 23993 - Posted: 21 Aug 2006, 2:21:53 UTC

Avi welcome to Rosetta!

I love the idea of creating some kind of tool, or toy or whatever to allow a person to manually move portions of the protein. Perhaps even tweak one that Rosetta is working on, and then have it continue after you\'re done and refine it! I would guess such a tool exists somewhere in the labs, because some folks still try to work these things out by hand... and, as with many things these days, \"by hand\" is often assisted by a computer. Even if just to view it.

I\'ve also been hoping for some sort of finer detail on the graphic to get a more atomic level understanding of what is being studied. They have talked about showing all of the \"side chains\" of the proteins, the presently just show the main backbone structure in the graphic. Not sure if this will help us to understand, or obscure some of what we see now. But they\'ve said it\'s coming.

I don\'t have any great low energy links for you. But I\'ll simply say that my understanding is that at each bond in the chain, there is an energy level, and if you succeed in optimizing all of them at the same time, you\'ll get a very low energy level, and probably be pretty close to the goal of predicting the native shape of the protein.

If you\'ll notice, the chains seem to wrap around themselves... if they get too far apart from each other, the bonds are weak... to tightly wrapped and low energy, where several strands are involved in the bond, are often found together.
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hugothehermit

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Message 24018 - Posted: 21 Aug 2006, 6:09:09 UTC

I\'ve got to say that would be fun, not much use to Rosetta@Home but, I know I\'d like to play with it, as long as all of the atoms are represented.

It would be kind of like a video game, who can get the lowest score :)
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Message 24102 - Posted: 21 Aug 2006, 15:08:58 UTC - in response to Message 24018.  

It would be kind of like a video game, who can get the lowest score :)

Not only that, but if you DID find the \"lowest score\"... well... you\'ve really FOUND something!

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Message boards : Rosetta@home Science : \"Do it yourself\" Protein Design



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