Modelling quantum transport from first-principles has proven to be a challenging task; debate continues as to the proper theoretical approach for treating electron currents across metal-molecule-metal junctions. Here, I will present an alternative physical scheme for transport at the many-body level and its implementation leading to calculation of IV curves for molecular scale systems. Systematic approximations can be derived from this higher-level theoretical treatment. The resulting computational scheme is applied to electron transport across several well-studied single molecules like benzene dithiol and short oligomer chains. All lead to results that compare well to the best experimental data available. The explicit treatment of electron-electron interactions allows us to investigate the extent of correlations beyond the single-particle picture and identify conditions for defining a ``best'' independent particle model for the tunnelling currents observed. We find that the most suitable single particle effective potential is not one commonly in use by electronic structure methods, such as the Hartree-Fock or Kohn-Sham approximations.