**1. Introduction**

The prediction of the three-dimensional structure of a protein, starting with the amino acid sequence, is still an unsolved issue. However a number of important advancements have been made and some methods offer solutions to this problem, specially when the target sequence has homologues whose structure has been determined. In any case, it is important to evaluate the quality of the prediction, as none of the methods offers assurance of success. The ROSETTA-design-HHMer (Rd.HMM) protocol stands out among the current quality assessment methods, because it offers evidence of the biological appropriateness of the prediction. In addition, Rd.HMM can be used to guide the modeling process towards the improvement of the model's quality. This chapter deals with the principles behind this protocol and gives practical advice on how to use the Rd.HMM to evaluate the quality of a three-dimensional modeled structure of a protein, and how to use the information to improve the model. The limitations of the protocol are also discussed.
