MultiMM

MultiMM reconstructs whole genome 3D chromatin structures using a multiscale molecular modeling approach based on OpenMM.

Key Features:

• Multi-scale energy minimization: Employs a multi-scale energy minimization strategy that captures chromatin's hierarchical structure.
• Hilbert curve initialization: Initiates simulations with a Hilbert curve-based structure.
• Integrator selection: Provides a large choice of numerical integrators for energy minimization.
• Nucleosome-resolution output: Produces nucleosome-resolution structures by making simplistic geometric assumptions about nucleosome structure and density on DNA.
• Chromosome-level output: Generates structure files for each chromosome.

Scientific Applications:

• Whole genome 3D structure reconstruction: Reconstructs the entire genome's structure within minutes for bioinformatics studies.
• Chromatin simulation: Simulates 3D chromatin structures incorporating nucleosome positioning, loops, compartments, or subcompartments.

Methodology:

MultiMM employs a multi-scale energy minimization strategy based on OpenMM, initiating with a Hilbert curve-based structure and allowing input files specifying nucleosome positioning, loops, compartments, or subcompartments.