TABLE 1

Quality of models as assessed by Modeller (Shen et al., 1995; Shen and Sali, 2006; Melo and Sali, 2007), ProQ (Wallner and Elofsson, 2003), and Procheck (Laskowski et al., 1993)

The MODELLER DOPE-score is a statistical potential energy-score trained to recognize correct folding by analyzing nonbonding interactions between atoms in a pair-wise fashion. The more negative the number, the higher the likelihood that a correctly folded model was obtained. The GA341 score is a statistical potential for correct local model geometry. Four parameters contribute to this score: backbone φ and ψ angles, atom overlap, atom probability density function, and exposed surface area. The score ranges between 0 and 1, where 1 is indicative of a correctly folded model. A ProQ LG score above 1.5 is indicative of a correct model; above 3, a good model; and above 5, a very good model. A MaxSub score >0.1 indicates a correct model, a score of >0.5 shows a good model, and >0.8 a very good model, whereby the LG score performs better with larger proteins such as P-gp and the MaxSub score is optimized for shorter proteins. ProCheck classifies dihedral angles in favorable, allowed, generously allowed, and disallowed regions of a Ramachandran plot.