What should be done if the modelled protein structure fails to pass VERIFY3D?

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Pawan Kumar

Hello,

If you are proceeding with a modeled structure (homology modeling), just check the validation score for the selected template. If the template is also showing that kind of score then try a different template and proceed with modeling.

Waqas Abbasi

My verify3d fails as there were no templates with a pass verify3d. Initially they were failing the Verify3D score at 30%. Through energy minimization and loop modelling i brought it up to 76 now. However it asks for 80% to be able to pass the 3d test.

I have done enough loop modelling, refinement, energy minimization, it is now stagnant at 76.

Please suggest how can i increase it more? Anyone?