Graph Measures Reveal Fine Structure of Complexes Forming in Multiparticle Simulations

Modern simulation techniques are beginning to be used to study the dynamic assembly and disassembly of multiprotein systems. In these many-particle simulations it can be very tedious to monitor the formation of specific structures such as fully assembled protein complexes or virus capsids above a background of monomers and partial complexes. However, such analyses can be performed conveniently when the spatial configuration is mapped onto a dynamically updated interaction graph. On the example of Monte Carlo simulations of spherical particles with either isotropic or directed mutual attractions, we demonstrate that this combined strategy allows for an efficient and also detailed analysis of complex formation in many-particle systems.