Compartment-guided assembly of large-scale molecular models with Bentopy

Area of Science:

• Computational Biology
• Biophysics
• Cell Biology

Background:

• Molecular dynamics simulations offer molecular insights into crowded cellular environments.
• Constructing starting configurations for large-scale cellular simulations is a significant challenge.

Purpose of the Study:

• To present bentopy, a novel workflow for generating cellular-scale models suitable for simulation.
• To address the bottleneck in creating complex starting configurations for molecular dynamics simulations.

Main Methods:

• Bentopy utilizes a voxel-based spatial representation for efficient molecule packing.
• The workflow supports the assembly of millions of molecules within complex cellular compartments.
• It enables the creation of models at both atomistic and coarse-grained resolutions.

Main Results:

• Bentopy successfully generated experimentally informed models across multiple biological scales.
• Demonstrated applications include a JCVI-Syn3A whole-cell model, a mitochondrion model, and a SARS-CoV-2 virion model.
• The workflow efficiently packs diverse molecular components into complex cellular structures.

Conclusions:

• Bentopy establishes a robust workflow for constructing simulation-ready cellular-scale models.
• It significantly accelerates the process of preparing complex biological systems for molecular dynamics simulations.
• This tool has broad applicability in cell biology and biophysics research.