I have used MODELLER to predict the tertiary structure of a protein, and I know that the next important step in homology modelling is validating the structure.
I know that there are tools such as SAVES and the validation tools provided by Swiss-Model. However, I am not sure if using online validation tools is sufficient enough to determine if the tertiary structure makes sense from a biological perspective, since they are based on statistics. Would using online validation tools and interpreting the results be sufficient enough to conclude that the protein structure is valid from a biological perspective? (I read in a post that the best way is to compare the protein structure against an experimentally determined structure, with regards to validating the structure, but in this situation there is no real structure).
I would really appreciate any insights as this is first time doing homology modelling. Thank you.