Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site

Table 1

The potential, given in equation (5), was used for these simulations of the phosphodiester backbone. The values for along with other parameters used to fit each of the 5 simulated line shapes in Figure 4 are given.

Label site	Fitting method	(kBT)	(kBT)	Amplitude (Å)	Jump rate (Hz)
G5	Manual	2.0	4.5	0.30	1 × 10^8	50°	1.73
	Automated	2.0	3.7	0.31	2.1 × 10^8	56°	1.13
C6	Manual	1.5	1.5	0.37	1 × 10^9	60°	1.66
	Automated	0.75	1.0	0.36	1.7 × 10^8	61°	1.31
G7	Manual	4.0	8.0	0.32	1 × 10^8	40°	8.44
	Automated	1.9	1.5	0.27	8.8 × 10^7	71°	3.91
C8	Manual	1.0	3.0	0.32	1 × 10^8	30°	2.67
	Automated	0.9	3.1	0.33	1.4 × 10^8	35°	2.46
5mC6	Manual	2.5	4.5	0.32	1 × 10^8	40°	2.74
	Automated	3.6	3.7	0.39	1.2 × 10^8	20°	1.82