Structure validation can be done by using the following methods

1. PROCHECK
2. PROCESS

PROCHECK

PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. The complete analysis is done by PDBsum. We need to upload our FASTA Sequence and perform FASTA search vs all sequences in the PDB to get a list of the closest matches. We get an output as follows:

We select the 1t1g(A) from the list and obtain the following output:

Clicking on the PROCHECK image we get the Ramachandran plot. Two torsion angles in the polypeptide chain also called Ramachandran angles describe the rotations of the polypeptide backbone around the bonds between N-Cα (called Phi, φ) and Cα-C (called Psi, ψ). A special way for plotting protein torsion angles was also introduced by Ramachandran and co-authors, and was subsequently named the Ramachandran plot. The Ramachandran plot provides an easy way to view the distribution of torsion angles in a protein structure. It also provides an overview of excluded regions that show which rotations of the polypeptide are not allowed due to steric hindrance (collisions between atoms). The Ramachandran plot of a particular protein may also serve as an important indicator of the quality of its three-dimensional structures.

Statistics of Ramachandran plot

There are different regions on the Ramachandran plot. The red color depicts the core region in which the most favorable phi and psi angles are possible. The yellow region shows the less possible confirmations and this is termed as the allowed region. Generous region is the green colored region in which a little lesser confirmations than the allowed region are possible. The grey color shows the non-allowed region where conformations are not allowed.
Ramachandran plot gives the most possible regions for the secondary structures. Thus, with the possible no.of phi psi angles a three-dimensional structure can be predicted.
A Complete report from the PROCHECK CAN be viewed here .

PROCESS

PROSESS (Protein Structure Evaluation Suite & Server) is a web server designed to evaluate and validate protein structures solved by either X-ray crystallography or NMR spectroscopy. Using PROCESS we submit our pdb file of the 3-D Model which we obtained from SWISS-MODEL. The results of the PROCESS show us some interesting results which are as follows:

We can see from the figure that our model has an overall quality of 5.5 with covalent bond quaity of 7.5, Non-Covalent/Packing Quality eqal to 6.5 and Torsion Angle Quality of 4.5. Looking at these statistics we can say that our model has a 50% chance of similarity with the 1t1g(A) protein. Also from the figure we can see that our structure has 28% helix , 30% beta-strand, 23% turn and 42% coil. There were no Homologus results were found. The protein length was found to be 339 for Chain A. The PROCESS results also provide the Structure Quality Categories and its influenecs on the resluts.
The whole set of PROCESS resluts can be viewed here