The computational prediction of the protein 3D structures involves the mathematical modeling techniques based on statistical terms. That is why the resultant structures may have some structural issues related to β-sheets, α-helices, non-structural loops, amino acid chain angles and backbone psi, phi bond angles that pose potential energy constraints in the structure. The validation of the computationally predicted structure is mandatory that compares different parameters of the protein 3D structure with that of experimentally available protein structures. Here, in this chapter we will discuss the evaluation procedure of the 3D structures for their accuracy and physiochemistry by numerous available tools.
Keywords: Anolea, ERRAT, Molprobity, PDBsum, Rampage, Structure evaluation.