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feet1st's picture
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Joined: 01/25/2008
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I found this link:
It lists all of the various amino acids and their level of hydrophobicity.

I haven't had a chance to try it out in the game yet, but I presume this will give you clues to indicate it's time to scrap this model and try a new one. I mean if you have a highly hydrophobic residue on the outside of your model, it's probably going to score better if you can wrap it differently.

But it is always a compromise, right? So you can see in the chart the ones with the strongest preference towards (-) or away from (+) water (the outside surface).

Any chance the hydrophobic view could be enhanced to colorize these reletive levels?? I mean make the more phobic residues a darker green, and more philic a darker blue for example.

Joined: 11/12/2007

This is a good idea. I'll talk with the biochemists to see if we can get at this information from within Rosetta to integrate this information into the game.

spvincent's picture
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Joined: 12/07/2007
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I'd also like to see a gradation of colour as suggested by feet1st.

But I'm a little puzzled by the hydrophobicity value assigned to tryptophan in that link, where it's indicated as being mildly hydrophilic. Isn't tryptophan supposed to be strongly hydrophobic, with a strong tendency to be on the inside of proteins?


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons