Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions

Abstract

The interior of living cells is densely filled with proteins and their complexes, which perform multitudes of biological functions. We use coarse-grained simulations to reach the system sizes and time scales needed to study protein complexes and their dense solutions and to interpret experiments. To take full advantage of coarse-graining, the models have to be efficiently implemented in simulation engines that are easy to use, modify, and extend. Here, we introduce the Complexes++ simulation software to simulate a residue-level coarse-grained model for proteins and their complexes, applying a Markov chain Monte Carlo engine to sample configurations. We designed a parallelization scheme for the energy evaluation capable of simulating both dilute and dense systems efficiently. Additionally, we designed the software toolbox pycomplexes to easily set up complex topologies of multi-protein complexes and their solutions in different thermodynamic ensembles and in replica-exchange simulations, to grow flexible polypeptide structures connecting ordered protein domains, and to automatically visualize structural ensembles. Complexes++ simulations can easily be modified and they can be used for efficient explorations of different simulation systems and settings. Thus, the Complexes++ software is well suited for the integration of experimental data and for method development.