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

Area of Science:

• Computational Biology
• Biophysics
• Molecular Dynamics

Background:

• Cellular interiors are crowded with proteins and complexes essential for biological functions.
• Simulating these dense biological systems requires advanced computational methods.
• Existing coarse-grained models need efficient and user-friendly simulation engines.

Purpose of the Study:

• Introduce Complexes++ simulation software for residue-level coarse-grained modeling of proteins and complexes.
• Provide a versatile tool for simulating dense protein solutions and interpreting experimental data.
• Facilitate method development in computational structural biology.

Main Methods:

• Utilized coarse-grained simulations with a residue-level model for proteins.
• Employed a Markov chain Monte Carlo engine for configuration sampling.
• Developed a parallelization scheme for efficient energy evaluation in dilute and dense systems.
• Introduced the pycomplexes toolbox for setting up complex topologies and simulations.

Main Results:

• Complexes++ software efficiently simulates protein complexes and their dense solutions.
• The pycomplexes toolbox simplifies the setup of multi-protein complexes and various simulation ensembles.
• The software supports flexible polypeptide growth and automatic visualization of structural ensembles.
• Demonstrated efficient simulation of both dilute and dense biological systems.

Conclusions:

• Complexes++ offers an efficient and adaptable platform for coarse-grained simulations of protein complexes.
• The software is well-suited for integrating experimental data and advancing simulation methodologies.
• Facilitates exploration of diverse simulation systems and settings for biological research.