Results from NR simulations of the cSIN2.

<p><b>A:</b> The number of unique complexes in independent simulations as a function of time: this curve represents the average over 15 independent simulations. In this panel, as with all other panels in this figure, the error bars represent confidence intervals. The steady-state number of unique complexes is slightly smaller for the cSIN2 than the original cSIN using constant nM affinities ( compared with ). <b>B:</b> This plot shows the probability of finding a complex of a particular size across the entire population of 15 simulations at the final time point in panel A. The distribution of sizes is similar to that found for NR simulations of the original cSIN, although the complexes are, on average, somewhat smaller than those obtained from NR simulations of the cSIN at . <b>C:</b> This plot displays the distance between independent simulations over time: the curve represents the average over all unique comparisons between 15 independent simulations using the distance measure defined in equation 5. The distances obtained from the cSIN2 are slightly lower than those obtained from the cSIN at ( vs. ). <b>D:</b> This curve represents the distance between simulations as a function of complex size, averaged over all unique comparisons between 15 independent simulations at the final time point in panel A. The overall shape of this curve is essentially identical to the nM case for the original cSIN as displayed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032032#pone-0032032-g005" target="_blank">Figure 5</a>; the main difference is that the simulations based on structure-derived 's sample somewhat smaller complexes than the original nM case.