cellPACK

cellPACK constructs three-dimensional mesoscale models by packing molecular components to represent biological environments at approximately 10–100 nanometers and by integrating structural and systems biology data.

Key Features:

• Modular Architecture: A modular framework that integrates multiple packing algorithms to generate coherent mesoscale models.
• Packing Algorithms: Implements and integrates existing and novel packing algorithms to place molecular components within three-dimensional volumes.
• Integration of Experimental Data: Incorporates data from systems biology and structural biology sources to inform component selection and placement.
• Predefined Recipes and Models: Provides recipes and models for blood plasma, cytoplasm, synaptic vesicles, HIV, and a mycoplasma cell.
• Validation Tools: Includes tools to validate and analyze model accuracy and reliability.
• Scripting-driven Packing Experiments: Supports scripting for automated packing experiments and reproducible model generation.
• Visualization and Analysis: Produces visualizable three-dimensional models amenable to downstream analysis.
• Hypothesis Testing: Enables modeling of molecular distributions, exemplified by studies of HIV envelope protein distribution for hypothesis testing against experimental observations.

Scientific Applications:

• Mesoscale Structural Modeling: Generation of mesoscale models to study structural systems biology at the 10–100 nm scale.
• Hypothesis Testing of Molecular Distributions: Modeling and analysis of spatial distributions of molecules such as the HIV envelope protein to compare with experimental data.
• System-specific Model Development: Creation and adaptation of recipes for specific biological contexts including blood plasma, cytoplasm, synaptic vesicles, HIV, and mycoplasma cell.
• Model Validation and Analysis: Validation and analytical assessment of assembled mesoscale models to evaluate accuracy and consistency with input data.

Methodology:

cellPACK assembles three-dimensional models by packing molecular components using modular packing algorithms, integrates systems biology and structural biology data to inform placement, supports scripting-driven packing experiments, and performs model validation and analysis.