The 3D protein structures were validated using RAMPAGE
Ramachandran plot and functional structures were predicted based on the homologous regions from other species including human, rat, mouse and panda.
Ramachandran Plot generated by RAMPAGE (http://mordred.bioc.cam.ac.uk) further vali-dated the modelled protein.
The modelled protein has to be validated and it is done by online server RAMPAGE (
Ramachandran Plot Analysis) based on an assessment of
Ramachandran Plot.
The model deriving from the SWISS-MODEL had energy and steric values raging between the values recorded for the other two mentioned strategies; therefore, the model resulting from MODELLER due to the adoption of the restriction method allowed the best steric evaluation results: 96.4% of the residues in favorable regions of the
Ramachandran plot. The global MODELLER measurement was also satisfactory, this model recorded normalized discrete optimized protein energy (zDOPE) score (-1.94), and it indicated that the atom pair distances in the model comply the distances recorded for a large sample of known protein structures; therefore, it was the model of choice (Table 1).
To validate the backbone conformation of the predicted structure, the Phi/Psi
Ramachandran plot was obtained through PROCHECK server (Laskowski et al., 2001).
Ramachandran plot for the normal pRB showed 91.7% residues in the favorable regions.
The reliability of predicted 3D structures of all the proteins of waxy genes were checked using
Ramachandran plot.
Ramachandran plots were finally obtained as homology model and template for quality assessment of 3D model.
The backbone conformation of the refined model was validated using
Ramachandran plot obtained through PROCHECK.
All the predicted protein structures were passed through quality analysis and structural validation by
Ramachandran plot assessment.