Z-score, RMSD (to what?) or Ramachandan may be viewed as a way of establishing if the homology model makes any sense. True validation can only be done by comparison to experimental data, like e.g. deltaG binding of ligands, ligand poses and interaction with selected residues (through mutagenesis data), low-resolution xray/nmr and so on.

Thanks Bartosz.....

Hi Thomson,

You can try the following links

http://mordred.bioc.cam.ac.uk/~rapper/rampage.php

https://services.mbi.ucla.edu/SAVES/

https://prosa.services.came.sbg.ac.at/prosa.php

Also, if you have modelled using MODELLER, then you can look into this link for more information on 'good' and 'bad' models

https://salilab.org/archives/modeller_usage/2010/msg00030.html

Thank you Sneha....

The stereochemical validation of model structures of proteins is an important part of the comparative molecular modeling process. Firstly, the selection of high quality structures for inclusion in loop dictionaries is important for the simple reason that these coordinate sets will be used to build future models. Secondly, the structural evaluation of comparative modeling output must be used to identify possible problematic regions.

https://proteinstructures.com/Modeling/Modeling/Modeling/model-quality2.html

Thanks Athar.....

2D-NMR analysis of the active site region can serve to verify that the HM is reasonable.

Thank you Lone.....

Apart for these very interesting and valuable recommendations of the researchers, I want to add one more link that may be helpful.

https://www.researchgate.net/post/How_to_validate_our_homology_model

Thanks.

thanks....