Hello Chakkyarath, 

The structure of proteins is resolved experimentally or computationally predicted in order to answer a specific question, such as how the protein catalyzed a reaction x. 

Protein model portal provides structural clues for researchers even for proteins without known structures. Sometimes meaningful information can be drawn from the structure model. 

Thus if your model provides important insights on the protein you might be able to publish the results.  Also note that even if your structure model explains something you may need to design and execute validation experiments to support your findings. 

Good luck. 

Cheers, 

Seungpyo 

It would be better to build your own homology model. However, if you are resolved to use someone else's model, make sure that it is well documented and (even better) published.