Analysis of biomolecular dynamics by FRAP and computer simulation

Methods Mol Biol. 2015;1251:109-33. doi: 10.1007/978-1-4939-2080-8_7.


We present a Monte Carlo simulation environment for modelling complex biological molecular interaction networks and for the design, validation, and quantitative analysis of FRAP assays to study these. The program is straightforward in its implementation and can be instructed through an intuitive script language. The simulation tool fits very well in a systems biology research setting that aims to maintain an interactive cycle of experiment-driven modelling and model-driven experimentation: the model and the experiment are in the same simulation. The full program can be obtained by request to the authors.

MeSH terms

  • Algorithms*
  • Diffusion
  • Fluorescence Recovery After Photobleaching / methods*
  • Models, Biological*
  • Molecular Dynamics Simulation*
  • Monte Carlo Method
  • Protein Binding
  • Systems Biology / methods*
  • User-Computer Interface