Understanding the influence of the cellular environment
on protein
conformations is crucial for elucidating protein functions within
living cells. In studies using molecular dynamics (MD) simulation,
carbon nanotubes and hydrophobic cages have been widely used to emulate
the cellular environment inside specific large biomolecules such as
ribosome tunnels and chaperones. However, recent studies suggest that
these uniform hydrophobic models may not adequately capture the environmental
effects inside each biomolecule. Based on these facts, it is necessary
to generate spherical and cylindrical models with varied chemical
properties corresponding to the components within target biomolecules.
We developed a biomolecular environment-mimicking model generator
(BEMM-GEN) that generates spherical and cylindrical models with user-specified
chemical properties and allows the integration of arbitrary protein
conformations into the generated models. BEMM-GEN provides model and
protein complex structures, along with the corresponding parameter
files for MD simulation (AMBER and GROMACS), and users immediately
run their MD simulation based on the generated input files. BEMM-GEN
can be freely downloaded and installed via a Python package manager
(pip install BEMM-gen). The source code files and a user manual for
operation are provided on GitHub (https://github.com/y4suda/BEMM-GEN).