Hello, I have created a homology model for a protein, where the seq. identity between the template and target is 40%. The template structure also contains co-factor and an inhibitor in bound form means it is a complex. I'll have to define the ligand binding site in target (homology model) based on inhibitor bound in template structure. But before to reach that stage, i want to simulate the created model to refine the structure which is a common practice in modelling. I'm not pretty sure that should i simulate the model structure along with the inhibitor and co-factor from template, or one of them, or just only the protein structure alone? Please let me, if you have any referenced answer.
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