Table 2.

Overview of the required model specifications and typical experiments for obtaining them. FCS, fluorescence correlation spectroscopy; FCCS, fluorescence cross-correlation spectroscopy; FRET, Förster resonance energy transfer; FRAP, fluorescence recovery after photobleaching.

Model parameter/specification	Typical experimental procedure
List of elementary molecules	Dependent on model assumptions and no specific experimental procedure
List of interaction rules	Yeast two-hybrid (Y2H), mammalian two hybrid (M2H), co-immunoprecipitation, tandem affinity purification, FCS, FCCS, FRET (see Section 2.4 for details)
Geometry of elementary molecules	Estimates based on molecular mass (see Section 2.3), or protein structure methods (X-ray crystallography [25,26], NMR spectroscopy [27,28], and Dual polarization interferometry [29])
Diffusion coefficient (D)	FCS, FCCS, and FRAP
Dissociation rate koff	FRAP, and FCS
Association kon	Based on koff and the relative concentration