The ratio between normalized affinity and normalized occupancy. We consider the smallest subsequence (46 Kbp) and consider the top ≈ 180 sites (the binding energy is not lower than 30% compared to the strongest site). Only lacI molecules were added to the system and 60 simulations were run for each set of parameters, each simulation was run for: 2000 s (in the case of 10 molecules), 200 s (in the case of 100 molecules) and 20 s (in the case of 1000 molecules). On the first row none of the parameters are changed, while on the second and third ones the number of lacI molecules and the association rate was varied according to the system size.
Zabet BMC Systems Biology 2012 6:121 doi:10.1186/1752-0509-6-121