ProNOI

ProNOI integrates atomic-style nano objects with biological macromolecules to generate composite models for simulating nano–bio interactions and electrostatic properties.

Key Features:

• Generation and customization: Generate geometrically precise atomic-style nano objects with customizable shapes, dimensions, and unlimited quantity and combine them with biological macromolecules in Protein Data Bank (PDB) format.
• Geometric positioning and sizing: Adjust shape, dimensions, and absolute position of nano objects within composite models to define spatial relationships with macromolecules.
• Charging and dielectric modeling: Assign specified surface or volumetric charge densities and user-defined dielectric constants to nano objects.
• Force field compatibility: Assign atom charges and radii for biological macromolecules using Amber, Charmm, OPLS, or PARSE force fields.
• Export formats: Export composite models in PQR format or PQRE when a default dielectric constant distribution is not selected.

Scientific Applications:

• Nano–bio interface studies: Model and analyze interactions at the nano–bio interface between nano objects and biomolecules.
• Biomaterials design: Design and evaluate composite biomaterials combining custom nano objects with proteins and other macromolecules.
• Drug delivery exploration: Explore structural and electrostatic aspects relevant to nano-enabled drug delivery systems.
• Protein–nano composite modeling: Construct composite assemblies embedding protein complexes such as the barnase-barstar complex within designed nano structures.

Methodology:

Generate atomic-style geometrical objects and integrate them with biological macromolecules in PDB format, assign surface or volumetric charge densities and user-defined dielectric constants to nano objects, assign atom charges and radii using Amber, Charmm, OPLS, or PARSE, and export resultant models in PQR or PQRE formats.