9. Validate and estimate model quality
Evaluate and estimate the quality of the structure. You can use the same tools as for experimental structures. Ramachandran plot can be investigated and analyzed with several tools. PROCHECK (Laskowski et al., 1993), WhatCheck (Hooft et al., 1996), MolProbity (Williams et al., 2018), Verify3D (Lüthy et al., 1992) and many other tools are available. Several of them can be run via SAVES (https://saves.mbi.ucla.edu/) to control stereochemical quality, bond angles, bond lengths, etc. At the Critical Assessment of protein Structure Prediction (CASP) challenges (https://www.predictioncenter.org/) the community has developed various tools and measures e.g. to compare structures with experimental structures.
One way to estimate usefulness of the model is to use it to interpret experimental data. If successful, the model can be useful also for other applications. Describe any details of such applications.
Example. The quality of the produced model was evaluated with PROCHECK (Laskowski et al., 1993) and MolProbity (Williams et al., 2018). Ramachandran plot (Ramachandran et al., 1963) indicated that 91% of the residues are on the most favored area and only two in disallowed region. Bond lengths and angles are well within normal ranges (on average 0.011Å and 2.1 degrees, respectively), the same with the torsion angles. According to MolProbity there are no clashes and there are not issues with geometry. The model was tested also by the Verify3D technique (Lüthy et al., 1992) and found to have the score of a typical globular protein.
As as functional test we evaluated the method in describing a known interaction based on a amino acid substitution. D304L in the lower lobe, was explained based on the model as having a structural effect originating from the disruption of a salt bridge with R244 in the upper lobe. The prediction is correct based on experimental data.