What are the basic parameters for validation of predicted proteins?
The predicted protein should have its functional domains intact.
In case they are not implicated previously to have a function, a quick functional validation in A. thaliana should be helpful.
If the chemical shifts, for the 13Ca or 13Cb nuclei are available, you can use the server
http://cheshift.com/
I suggest you also to use PROCHECK and WHATIF
You say predicted protein. Did not mention whether you are designing an algorithm or just using an algorithm to predict.
In case of protein structure prediction each different server follows somewhat different algorithm and so do the parameters vary regarding the same. So, the algorithm you use must obviously come up with some threshold parameters justifying how well the structure been predicted. You can say that as the prediction accuracy per server kind of thing.
Jorge, above, have given you few nice examples regarding server.
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