PyRID

PyRID simulates reacting and interacting particles in biological systems using Brownian dynamics, enabling analysis of molecular organization and protein interactions from individual proteins to polydisperse substrates.

Key Features:

• Reaction simulation: PyRID simulates unimolecular and bimolecular reactions.
• Pair interactions: PyRID simulates pair interactions to assess dynamics of individual interacting proteins and polydisperse substrates consisting of many different molecules.
• Compartment and surface diffusion: PyRID supports mesh-based compartments and surface diffusion of particles.

Scientific Applications:

• Protein interaction analysis: PyRID enables analysis of dynamics resulting from individual interacting proteins to polydisperse substrates consisting of many different molecules.
• Membrane protein interaction studies: PyRID enables analyses of the interaction between (trans-)membrane proteins with intra- and extracellular proteins.
• Molecular organization analysis: PyRID supports features for analyzing molecular organization in biological systems.

Methodology:

PyRID uses Brownian dynamics simulation methods implemented entirely in Python.