Usually we can prepare homology model, but problem comes in their evlaution. What are various ways to evaluate the homology model?
The validation is the most important steps in homology modeling, crude models obtained has to be validated. For this purpose,
1) SAVES server (http://nihserver.mbi.ucla.edu/SAVES/) from NIH MBI Laboratory is mostly useful for analysis.
The quality can be evaluate using PROSA, VERIFY3D, ERRAT, and AMOEBA.
You can also do loop modeling using ModLoop module available in Modeller depending on your model.
2) Again calculate the RMSD between template PDB and homology model to check how your model is deviated from the original PDB stucture.
3) The most important issue is the active site so please go through the literature and find out the amino acid residues involved in the active site of the same class of protein. In each class there are few conserved amino acid residues are present which are mainly involved in the catalysis. The orientation and the conformations of these residues plays an important role in catalysis. If everything goes well then you are on the safe side otherwise you have to refine it again and again to achieve the goal.
4) Do the energy minimization using any one of the available software but be careful that overall structure should not be altered.
You can validate the model using SAVes server(includes procheck,verify3D,errat,prove results). You may also use ProSA web server for determining the overall quality of the model. ModLoop may be used for loop modeling and the fold analysis can be done by using TM-align. MD simulations can be done for analyzing the stability of the model.
Best Regards,
The validation is the most important steps in homology modeling, crude models obtained has to be validated. For this purpose,
1) SAVES server (http://nihserver.mbi.ucla.edu/SAVES/) from NIH MBI Laboratory is mostly useful for analysis.
The quality can be evaluate using PROSA, VERIFY3D, ERRAT, and AMOEBA.
You can also do loop modeling using ModLoop module available in Modeller depending on your model.
2) Again calculate the RMSD between template PDB and homology model to check how your model is deviated from the original PDB stucture.
3) The most important issue is the active site so please go through the literature and find out the amino acid residues involved in the active site of the same class of protein. In each class there are few conserved amino acid residues are present which are mainly involved in the catalysis. The orientation and the conformations of these residues plays an important role in catalysis. If everything goes well then you are on the safe side otherwise you have to refine it again and again to achieve the goal.
4) Do the energy minimization using any one of the available software but be careful that overall structure should not be altered.
Dear Arvind,
As Gaurao points out nicely, you need to know as much as possible about the protein of interest. This will help you in understaning the model plus it gives you an idea wich areas are important for its function. I have experience with all sorts of homology modeling programs, and for the record, each program gives slightly different results. Therefore using different software programs is advisable. These results should than be run by (offcourse) different evaluation programs. Some have already been mentioned, but protcheck and whatcheck are also good ones. In the end, you should use the model that has the best RMSD score. Keep in mind though, RMSD score are based on PDB. So if there isnt a good match between your protein and the pdb, rmsd can be misleading.
Good luck and if you need any help please contact me.
René
The best way to evaluate your model is through statistical potentials. For example, if your structure is in PDB format, ProSA (https://prosa.services.came.sbg.ac.at/prosa.php) evaluates your model and tells you which regions are energetically unfavorable (i.e. incorrectly modeled).
The energy of the template and homology model should be very close. see the link
https://www.researchgate.net/publication/248382055_Cystathionine__Lyase_like_Protein_with_Pyridoxal_Binding_Domain_Characterized_in_Leishmania_Major_by_Comparative_Sequence_Analysis_and_Homology_Modelling
Article Cystathionine β Lyase like Protein with Pyridoxal Binding Do...
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