Understanding electron transport processes in molecular wires connected between contacts is a central focus in the field of molecular electronics. Especially, the dephasing effect causing tunneling-to-hopping transition has great importance from both applications and fundamental points of view. We analyzed coherent and incoherent electron transmission through conjugated molecular wires by means of density functional tight-binding theory within the D'Amato-Pastawski model. Our approach can study explicitly the structure/transport relationship in molecular junctions in a dephasing environmental condition using only a single dephasing parameter. We investigated the length dependence and the influence of thermal fluctuations on 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.