To validate the backbone conformation of the predicted structure, the Phi/Psi Ramachandran plot was obtained through PROCHECK server (Laskowski et al.
Ramachandran plot and % of the residues in the core region, allowed regions and in the disallowed region are shown in Fig.
Ramachandran plot was conducted using PROCHECK (Laskowski et al.
A1) Homology-based 3D model of T1 (c3k07A), (A2)
Ramachandran plot of c3k07A, (A3) Z score plot of c3k07A; (B1) Homology-based 3D model of T2 (d3dtua), (B2)
Ramachandran plot of d3dtua, (B3) Z score plot of d3dtua; (C1) Homology-based 3D model of T3 (c2zjsE), (C2)
Ramachandran plot of c2zjsE and (C3) Z score plot of c2zjsE
The reliability of predicted 3D structures of all the proteins of waxy genes were checked using Ramachandran plot.
For rice accessions, 3D model was constructed using Swiss model and reliability of 3D model was confirmed using Ramachandran plot (Fig.
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.
Verification and validation of the model by PROCHECK,
ramachandran plot, ERRAT value and verify-3D
All the predicted protein structures were passed through quality analysis and structural validation by
Ramachandran plot assessment.
PROCHECK was used to analyze the
Ramachandran plot of the model by comparing it with the
Ramachandran plots of 163 representative structures solved at high resolution of at least 2.
Selection of most accurate model was done by calculating Z-score for overall quality of model by ProSA-web and
Ramachandran plot by PROCHECK (Table VI).
By attaining the measurements of the [PHI] and [PSI] angles,
Ramachandran plots were constructed using linear, globular, sheeted and helical protein structures.
