BEMM-GEN

BEMM-GEN generates biomolecular environment-mimicking models with user-specified chemical properties for molecular dynamics simulations of proteins in complex cellular environments.

Key Features:

• Spherical and Cylindrical Model Generation: Creates spherical and cylindrical models with varied chemical properties corresponding to components within target biomolecules.
• Protein Conformation Integration: Integrates arbitrary protein conformations into the generated environment models.
• MD Simulation Input File Generation: Provides model and protein complex structures with corresponding parameter files for AMBER and GROMACS molecular dynamics simulations.

Scientific Applications:

• Cellular Environment Simulation: Emulates the heterogeneous chemical environment inside large biomolecules such as ribosome tunnels and chaperones, addressing limitations of uniform hydrophobic models like carbon nanotubes and hydrophobic cages.
• Protein Function Elucidation: Enables investigation of how cellular environments influence protein conformations and functions within living cells.

Methodology:

BEMM-GEN generates spherical and cylindrical models with user-specified chemical properties and integrates arbitrary protein conformations into these models, producing structure and parameter files for MD simulation.