To analyze DNAse 1 footprint data, the fortran module must describe the dependent variable, the observed protection against nicking by DNAse 1, as a function of the independent variable, the active concentration of protein ligand. One needs to bear in mind the following concepts to understand how the module for analyzing DNAse 1 footprint data works.
Fractional protection is linearly related to fractional occupancy.
Because it is always best to treat raw data rather than transformed data in a nonlinear regression analysis, the fortran module must include these limits as parameters to be determined during the anlaysis. Fractional occupancy can be modeled as a function of free ligand concentration and Gibbs free energies of the various states in which a given site is occupied. Note that state 0, in which no lignads are bound, is taken as the reference state whose dG value is arbitrarily set equal to zero. The dG values for the remaining states are comprised of the reference state value plus any other relevant free energies. For example, in a three site system state 4 has sites 1 and 2 occupied.