We typically look at I_sc. I_sc is the “interface score,” which is the total score of the complex minus the sum of the scores of the individual docking partners. Values of about -5 to – 10 typically indicate a good decoy. It is important to also look at the total score, as a clash or other problem in one of the partners can distort the I_sc significantly. These problems are most common when incorporating flexible backbones into docking.
That web page is still what we recommend using, however the scripts used haven’t been ported to work with Rosetta 3 yet, so they may need to be tweaked a bit. If you run into specific problems, please post them. Finally, totally blind predictions haven’t been thoroughly tested in Rosetta 3, so please keep that in mind as you procede.