There aren't any Zika virus solved protein structures. I'm proposing to use homology modelling to create some stand-ins until such times as the real thing can be produced. The templates could be various flaviviruses - at the moment I think that dengue is the best bet for most proteins. Around two-thirds of the proteins could be modelled. The models could be used to examine the functional/structual implications of any clade-specific substitutions.
I'd like to consult the community on which Zika genome to model. I've been following the conversations on the site about unreliability of some deposited sequences. Normally, for something like this, I'd choose a reference genome for the basic homology model and then locally model substutions in newer genomes. However, I gather that the reference genome MR766 is probably not the best starting point.
Any suggestions much appreciated.