Four Flavivirus NS1 protein models based on ZIKV-UG (Zika virus from Uganda), ZIKV-BR (Zika virus from Brazil), DENV2 (Dengue virus variant 2), and WNV (West Nile Virus). Due to missing regions in the crystals of these four NS1s (i.e., X-ray structures with PDB IDs 5K6K, 5GS6, 4O6B, and 4O6D, respectively), a homology protocol was applied. Models were built with Modeller 9.24 using default parameters, and the models with the best DOPE score were selected. NS1ZIKV-UG and NS1ZIKV-BR models are based on the templates with PDB ids 5K6K and 5GS6, respectively. For NS1DENV2, three templates were used: the two complete structures from NS1ZIKV-UG and NS1ZIKV-BR, and the crystal PDB ID 4O6B. For NS1WNV, the same strategy was followed as for NS1DENV2, but the third template was changed for the crystal PDB ID 4O6D. For more details, check the SI of https://doi.org/10.1016/j.virusres.2022.198838.