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.
Rampage server was used for the validation of 3d structure modeled by plotting Ramachandran plot
(Ramachandran GN, et al.
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).
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.
Validation was performed by evaluating the stereochemical feasibility of the torsion angles using the Ramachandran Plot
(RP), (14) generated using the graphic package Ramachandran Plot
(version 2) hosted on Indian Institute of Science, Bangalore server.
All the predicted protein structures were passed through quality analysis and structural validation by Ramachandran plot
PROCHECK analysis of the model for T1 exposed that, at resolution 3.52 [Angstrom] and R-factor of0.239, Psi-Phi pairs in Ramachandran plot