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. 2011 Jul 6;39(19):8281–8290. doi: 10.1093/nar/gkr531

Figure 3.

Figure 3.

Thermodynamic cycle for binding affinity calculations. The difference in the binding affinity between the transcription factor and two different DNA sequences is given by ΔΔGbind = ΔG3−ΔG4. According to the thermodynamic cycle ΔΔGbind can also be calculated via the alchemical pathway ΔG1−ΔG2.