Dresden 2011 – scientific programme
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BP: Fachverband Biologische Physik
BP 2: Protein Structure \& Dynamics
BP 2.5: Talk
Monday, March 14, 2011, 11:45–12:00, ZEU 260
Using Graph Measures to Observe Complex Formation in Multiparticle Simulations — Florian Lauck1,2 and •Tihamer Geyer1 — 1Center for Bioinformatics, Saarland University, Saarbrücken — 2Dep. of Bioengineering and Therapeutic Sciences, UC San Francisco, CA, USA
Modern simulation techniques are beginning to study the dynamic assembly and disassembly of multi-protein 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.