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. 2019 Mar 8;9(3):145–159. doi: 10.15171/bi.2019.19

Table 1. The modeling validation assays using different online web-servers .

Methods Assay scheme Score Range
ProSA-web Modeling verification by calculating an overall quality Z-score - 3.45 NPS*
ERRAT (%) The overall quality for non-bounded atomic interactions 91.65 >50%
VERIFY3D (%) The number of residues having an average 3D/1D score above 2.0 72.00 >80%
RAMPAGE (%) The residues within the allowed region in psi/phi Ramachandran plot 98.60 >90%

* Native protein size (NPS): This criterion checks the z-score of the target structure whether is within the range of scores typically identified for the native proteins of similar size.