Model Validation Using Online Servers

We can visualize the geometiy of bond lengths, bond angles, dihedrals, etc. by choosing the required option from the drop-down menu of the check option (Figs. 5.53 and 5.54). 

The report for the Ramchandran plot can be generated by clicking on the report button (Fig. 5.55). 

The best model among the generated models can be saved separately by choosing the save option in the file menu of the MOE window. We can save the model in. pdb format. 

This model can further be evaluated through the online available servers like procheck [35], what if [36], etc. 

Structural Analysis and Verification Server (SAVES) [37] is the widely used server for the validation of the protein models. It has options like ERRAT [38], VERIFY 3D [39], PROCHECK, etc. which have specific evaluating methods described in the website itself (Fig. 5.56). 

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