backbone-independent density

[Anonymous]

Hello everyone!

Is it possible to get backbone-independent density for amino acid as a continuous function of rotameric chi[1-4] using some classes from dunbrack namespace? As shown in the picture A http://dunbrack.fccc.edu/bbdep2010/Tutorial.php#TraditionalLibrary

If it’s possible, please give me any hint or example what should I use.

Thanks in advance

[Anonymous]

To my knowledge, Rosetta only contains the backbone dependent version of the Dunbrack library – so I don’t think there’s a way to get the backbone independent version of it.

You can certainly get the Dunbrack energy of a residue as you vary the side chain chis (just create a pose with a single residue, change the chis and rescore), but it doesn’t sound like that’s what you want.

The data that Rosetta has for the Dunbrack 2010 library is in main/database/rotamer/ExtendedOpt1-5/ and is limited to probability, chi centers and standard deviation for each rotamer. You might be able to process that into what you’re interested in, but from my hazy impression at what you’re trying, I’m guessing you’ll be better off going directly to the data the Dunbrack lab releases, rather than trying to pass it through Rosetta first.

 

[Anonymous]

Yes, I was in a bit of a hurry and started this topic before I spotted within source that “the Dunbrack bbind library is not implemented in rosetta”.

>You can certainly get the Dunbrack energy of a residue as you vary the side chain chis (just create a pose with a single residue, change the chis and rescore), but it doesn’t sound like that’s what you want.

Yes, I checked such way, it is not what I wanted. 

>probability, chi centers and standard deviation for each rotamer

It is almost enough, but I have been a little confused how to do an interpolation with such data for a given chi with dependence on other chis in residue. However I have solved this problem throw interpolation of raw density traces for the rotamer data.

Anyway, many thanks for the answer.

 

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