Rosetta DNA – Protein-DNA scoring function and binding energy

[Anonymous]

Dear All,

I am new in using rosetta DNA application. I have run the score demo included in the protein_dna_interface_design example. I have some questions about the use of the tool and the output. I wonder if someone could please give me some directions. The demo includes a pdb file called 2h7h.pdb and after running the script score.script the programme outputs a file called score_2h7h_0001.pdb, which is a modified pdb file containing data about energy calculations (all listed in REMARK records). The first lines of this pdb file describe the weights used to calculate the total energy. I revised the supplemental material of the paper J. Mol. Biol (2004) 344, 59, and read that the weights listed there are not the same and that in the pdb file there are additional values. Is there any reference to revise about these weights?
The total energy reported in the output pdb file is the total energy for the entire protein-DNA complex. Is there a way to obtain the binding energy from the data saved in this file?
On the other hand, I need to make several runs of energy calculations. What option must I specify in order to run a list of pdb files?

I would be very grateful if you could help me with these questions.

Regards

Tomas

[Anonymous]

Rosetta’s scorefunction will have shifted a bit since a 2004 publication. It’s been rewritten pretty much from scratch since then, although we kept it more-or-less equivalent. I’ve asked the DNA guy to weigh in on the scorefunction changes.

Generally you can’t calculate binding energies from total energies. Cross-interface energies (binding energies) are lumped in with within-chain interactions, as PDB output stores only per-residue scores. Try running your complex through the InterfaceAnalyzer executable. I’ve never tried it on DNA but it’s worth a shot. You’ll probably need to figure out what scorefunction your DNA example is using (you have the weights, which you can convert into a weights file, or check against the existing weight sets in database/scoring/weights).

For most executables, you can either pass multiple PDB inputs to -s (-s one.pdb two.pdb three.pdb) or put them in a file:

one.pdb
two.pdb
three.pdb

and pass that file to -l (-l name_of_file). I don’t know which executable you are using but this works for most.

[Author]

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