Evaluating models with procheck
Hello
My name is Herbert Venthur, I'm PhD student from Universidad de La Frontera, Chile. I'm new and beginner with modeller, however, I can model a protein structure using the basic tutorial of modeller. The model structure that I have, I submitted to ProCheck to evaluate the model, my question is: Results indicate a 95% of residues in favoured regions. That valuew, it is enough to have a suitable model?, Could I perform a docking with this model then?
Thank your very much Best regards Herbert
On 05/17/2013 12:42 PM, HERBERT MAX VENTHUR PE¥A wrote: > I submitted to ProCheck to evaluate the > model, my question is: Results indicate a 95% of residues in favoured > regions. That valuew, it is enough to have a suitable model?, Could I > perform a docking with this model then?
You can't tell for sure, since it's very easy to make models where all the residues are in favored regions but that are still terrible models! (For example, a completely extended chain would probably score pretty well with this metric.) We usually recommend using an assessment method designed to test models (as opposed to real crystal structures). If using Modeller, we recommend normalized DOPE: http://salilab.org/modeller/9.11/manual/node198.html
Ben Webb, Modeller Caretaker
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HERBERT MAX VENTHUR PE¥A -
Modeller Caretaker