Protein modelling with modeller

Question

[Shamim Sarhadi]

Hi I am a newbie in protein modeling, I create a model for my aa sequence with modeller and I-TASSER (zhang lab server), now I have two models with different sequence, the model from I-TASSER has the same sequence with my target ,but the model from Modeller has different sequence in some area of sequence. I know there is different approach for modelling with these tools, but I want to know, can I report the model from modeller in my paper whereas it has some different in sequence from my target protein?

Thank you

[João Rodrigues]

MODELLER should build a structure of YOUR sequence using the structure you chose as a template and an alignment between YOUR sequence and the sequence of the template. If your model has a different sequence, something is wrong with your input..