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Neurotransmitter:sodium symporters are located on presynaptic neurons and terminate neurotransmission by removing the monoamine substrates from the synaptic cleft. Until very recently, only several conformational snapshots/structures of a bacterial homolog of neurotransmitter:sodium symporters, namely, the leucine/alanine transporter LeuT from Aquifex aeolicus, were available. However, this transporter shares only 21b % overall sequence identity with its human homologs. In this chapter, we describe how a model can be developed from a template with such low identity. The effort of model building will strongly depend on the purpose. We discuss this process and focus on the important steps that allowed us to obtain a model which can be used for molecular dynamics simulations. Furthermore, we also highlight the inherent limitations of the proposed approaches. Prediction of ligand binding brings in additional complexity. Therefore, experimental scrutiny of the resulting models is a key component to successful validation. We describe two specific examples: model building of the dopamine transporter and ligand docking to the serotonin transporter. We evaluate our modeling approach by direct comparison of our models to the recently published first eukaryotic neurotransmitter:sodium symporter, the drosophila melanogaster DAT transporter.