I have done protein-protein docking using rosetta 3.2 to generate 60,000 structures. I'm a bit confused about the next steps.
1) Which score, the total score or I_sc, to use for picking solutions for further consideration? Which of these are referred to in publications?
2) one of the older webpages I found describes three methods for picking solutions (http://graylab.jhu.edu/~mdaily/tutorial/blind_main.html). Are these still followed as a general procedure by the community?
Any help would be appreciated.