Recent work has shown that different theoretical approaches to the dynamics of the Susceptible-Infected-Susceptible (SIS) model for epidemics lead to qualitatively different estimates for the position of the epidemic threshold in networks. Here we present large-scale numerical simulations of the SIS dynamics on various types of networks, allowing the precise determination of the effective threshold for systems of finite size N. We compare quantitatively the numerical thresholds with theoretical predictions of the heterogeneous mean-field theory and of the quenched mean-field theory. We show that the latter is in general more accurate, scaling with N with the correct exponent, but often failing to capture the correct prefactor.