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

Table 2

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

Label site	Fitting method	(kBT)	(kBT)	Amplitude (Å)	Jump rate (Hz)
A4	Manual	6.0	6.0	0.25	2 × 10^8	20°	7.85
	Automated	8.8	6.7	0.16	1.8 × 10^8	61°	3.53
G5	Manual	4.5	4.5	0.27	3 × 10^8	20°	1.32
	Automated	1.5	2.3	0.17	8.6 × 10^7	60°	1.02
G7	Manual	6.0	6.0	0.25	2 × 10^8	20°	2.14
	Automated	5.1	15.3	0.18	7.2 × 10^7	75°	1.17
A10	Manual	4.5	4.5	0.27	1 × 10^9	20°	14.0
	Automated	0.19	0.13	0.19	9.7 × 10^7	60°	3.30