Fig. 3
PspA1-5c+p modeling, refinement, validation, and prediction of the conformational B-cell epitopes. a The I-Tasser 3D homology modeling of the PspA1-5c+p construct before and after refinement was displayed by PyMol v.2.5 software. Each domain is indicated in color. Validation of the model before and after refinement using b ProSA Web, c Ramachandran plot, and d ERRAT plot. The ProSA Web analysis shows the z-scores of − 4.41 and − 5.14 before and after refinement, respectively, and the plot of the residue scores showing local model quality by plotting energies as a function of amino acid sequence position is also shown. Ramachandran plot analysis after refinement showed 92.4%, 6.4%, and 1.2% of PspA1-5c+p protein residues were in preferred, valid, and non-valid (outlier) regions, respectively. In general, positive values correspond to problematic or erroneous parts of the input structure. The overall quality score of the selected model before and after refinement is 89.66% and 98.14%, respectively, using the ERRAT2 server. These values are expressed as the percentage of the protein for which the estimated error value falls below the 95% rejection limit. Two lines in the error axis reveal the confidence with which it is possible to eliminate areas that exceed this error value. Good high-resolution structures generally produce values around 95% or higher. e The conformational B-cell epitopes using the Elipro server on a refined and validated final 3D PspA1-5c+p model were predicted to be located in seven conformational B-cell epitopes. The conformational B-cell epitopes are shown in yellow and the gray parts are the rest of the residues