Rosetta residue design for DNA binding

The reference weight is just another scoreterm. You can just use the Reweight subtag to reweight the term to whatever you want it to be. http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/RosettaScripts_Documentation#SCOREFUNCTIONS That would scale all the reference weights, though. If you wanted to tweak the Arg reference weight specifically, you would have to modify the weights file itself. (Remember that if you use a scorefunction other than the default score12, you’ll need to set the movers/filters tag to use it.)

All that said, I don’t think that the reference weight is your main problem. Rather, I’m guessing that Rosetta isn’t correctly calling all the favorable interactions that the residue is making. You may need to bump up the sampling (for example, try -ex3 and -ex4 to increase sampling on the chi 3 and 4) to get rotamers in the correct orientation to make the good hydrogen bonds.

The other approach is that since you know those residues have to be Arg, you can force in that identity by using something like a resfile, or a TaskOperation which would limit design at that position.

Hi there,
The problem you are describing is a persistent one, Rosetta is better at handling hydrophobic interactions than highly charged interactions like those found at a protein DNA interface. As others have pointed out, this probably won’t be corrected by tweaking reference energies. That said, there are a couple of easy things you can do to try and remedy the situation. If you are not already, I would recommend pre-relaxing your input structure using Rosetta Relax application. Sometimes Rosetta dislikes good interactions because of minor unfavorable interactions with nearby residues that are not being redesigned or repacked.

A more sophisticated workaround should appear in the 3.5 release using something known as MotifDnaPacker. This approach supplies Rosetta with a database of canonical protein-DNA interactions that are found in the PDB, and provides a score term bonus for incorporating similar interactions in interface designs. (See http://www.ncbi.nlm.nih.gov/pubmed/22426128 details).

I guess the most direct answer is that we don’t HAVE a scorefunction premade for your purpose, other than the one that Justin’s DNA code is already using. Devising scorefunctions for various different simulations is an ultrahard problem: for one, we know that real physics has exactly one scorefunction, so using specialized ones is cheating, and for two, determining what the scorefunction should be for any particular simulation is something we can’t do with great reliability.

If you wanted to try to create the perfect scorefunction for DNA-protein interfaces, you’d need to generate DNA-protein interfaces with Rosetta, express the proteins, crystallize them, use the differences between the crystal and the model to fix the scorefunction, and cycle through this indefinitely until you had a perfect solution. This is obviously untenable. For some problems we attempt to short-circuit this by running models of known crystal structures with different scorefunctions until we find a scorefunction that best recapitulates crystals, but this isn’t particularly successful.

Manually hacking around with the scorefunction (in your case, by respecifying just the ARG weight in the reference energies) is a perfectly valid way to improve your simulation. It’s laborious and error-prone, exactly like all the other methods for improving scorefunctions.