By modeling research systems as complex systems we generalize similarity measures used in the literature during the last two decades. We propose to use the mathematical tools developed within the spin-glasses literature to evaluate similarity within systems and between systems in a unified manner. Our measure is based on the 'overlap' of disciplinary profiles of a set of research systems and can readily be integrated in the framework of traditional bibliometric profile analysis. The investigation of the distribution of the overlaps provides useful insights on the dynamics of the general system, that is whether it converges toward a unique disciplinary structure or to a differentiated pattern. We illustrate the usefulness of the approach by investigating the dynamics of disciplinary profiles of European countries from 1996 to 2011. We analyze several bibliometric indicators (including publications and citations) of European countries in the 27 Scopus subject categories. We compare the disciplinary profiles of European countries (i) among them; (ii) with respect to the European standard; and (iii) to the World reference. We find that there is a convergence toward a unique European disciplinary profile of the scientific production even if large differences in the scientific profiles still remain. The investigation of the dynamics by year shows that developing countries are converging toward the European model while some developed countries are departing from it. © 2014 Elsevier Ltd.