I am trying to find the the template against a sequence. The template I have found so far has less similarity with the structures known in the existing Databases. Can anyone help me out deciding that if I have more than 34% similarity,Can I model it by using Modeller and taking into account the modeller objective Function? I need help to interpret Modeller objective Function in regards to the subject cited above.
You can't know for sure if a template with 34% sequence identity will give a reliable model, of course (you'd need to know the native structure of the model to know that) but from past studies you can be reasonably confident that the model will be OK. The objective function tells you nothing of value here though, since like any energy function, it can only rank models built with the same sequence and set of restraints. You could build models using different templates, however, and use a assessment method (such as GA341 or PROSA) to get a rough idea of their relative qualities.
Ben Webb, Modeller Caretaker
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