  Computational prediction of protein structures is a difficult task, which
involves fast and accurate evaluation of candidate model structures. We propose
to enhance single model quality assessment with a functionality evaluation
phase for proteins whose quantitative functional characteristics are known. In
particular, this idea can be applied to evaluation of structural models of ion
channels, whose main function - conducting ions - can be quantitatively
measured with the patch-clamp technique providing the current-voltage
characteristics. The study was performed on a set of KcsA channel models
obtained from complete and incomplete contact maps. A fast continuous
electrodiffusion model was used for calculating the current-voltage
characteristics of structural models. We found that the computed charge
selectivity and total current were sensitive to structural and electrostatic
quality of models. In practical terms, we show that evaluating predicted
conductance values is an appropriate method to eliminate modes with an occluded
pore or with multiple erroneously created pores. Moreover, filtering models on
the basis of their predicted charge selectivity results in a substantial
enrichment of the candidate set in highly accurate models. In addition to being
a proof of the concept, our function-oriented single model quality assessment
tool can be directly applied for evaluation of structural models of
strongly-selective protein channels. Finally, our work raises an important
question whether a computational validation of functionality should not be
included in the evaluation process of structural models, whenever possible.
