Understanding electron transport mechanisms on the molecular scale is a central issue in the field of molecular electronics. Among them, the dephasing effect, causing the tunneling-to-hopping transition, has a great importance for applications as well as from the fundamental point of view. In this study, we analyzed the coherent and incoherent electron transmission through conjugated molecular wires by means of a first principle approach within D'Amato-Pastawski model. Our approach can study explicitly the structure/transport relationship in molecular junctions in a dephasing environment using only a single tuning parameter. We investigated the length dependence and the influence of thermal disorder on the transport and reproduced the well-known tunneling-to-hopping transition. This approach will be a powerful tool for the interpretation of recent conductance measurements of molecular wires.