A suite of computer programs has been developed under the general name Thetis, for monitoring structural changes during molecular dynamics (MD) simulations on proteins. Conformational analysis includes estimation of structural similarities during the simulation and analysis of the secondary structure with emphasis on helices. In contrast to available freeware dealing with MD snapshots, Thetis can be used on a series of consecutive MD structures, thus allowing a detailed conformational analysis over the time course of the simulation.