There are many stable conformations of a protein that govern it's function. Various structure prediction algorithms need to take into account all these stable conformations before predicting the structure of a protein. Recently, Mark C. et al.(2018) have developed an algorithm which takes care of all the ensemble of structure of proteins to predict it's function.
Their results show that while it's easier to model protein with one loop. It becomes difficult when it comes to modelling of different kind of proteins with multiple loops. Their results have shown that current methods being used for structure predictions are not suited for proteins with diverse conformations and having functionally important regions.
Marks C. et al.(2018) Predicting loop conformational ensembles. Bioinformatics 34(6) 949-956.