| Autor: |
Linke, Max, Quoika, Patrick K., Bramas, Berenger, Köfinger, Jürgen, Hummer, Gerhard |
| Předmět: |
|
| Zdroj: |
Journal of Chemical Physics; 11/28/2022, Vol. 157 Issue 20, p1-10, 10p |
| Abstrakt: |
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. [ABSTRACT FROM AUTHOR] |
| Databáze: |
Complementary Index |
| Externí odkaz: |
|
