  The SARS-CoV-2 spike (S) protein facilitates viral infection, and has been
the focus of many structure determination efforts. Its flexible loop regions
are known to be involved in protein binding and may adopt multiple
conformations. This paper identifies the S protein loops and studies their
conformational variability based on the available Protein Data Bank (PDB)
structures. While most loops had essentially one stable conformation, 17 of 44
loop regions were observed to be structurally variable with multiple
substantively distinct conformations based on a cluster analysis. Loop modeling
methods were then applied to the S protein loop targets, and the prediction
accuracies discussed in relation to the characteristics of the conformational
clusters identified. Loops with multiple conformations were found to be
challenging to model based on a single structural template.
