It would be of great interest to relate DWMs with a more biophysical binding-energy model of protein-DNA interactions.
In [ 15], Wang and colleagues proposed a new biophysical model of protein-DNA interactions, BayesPI2+, to model protein-DNA interaction.
On the one hand, detailed structural modeling of protein-DNA interactions has been used to calculate sequence dependent protein DNA interaction free energies [ 36].
Following the standard thermodynamic model of protein-DNA binding [ 42- 44], the probability of this event is dependent on the number of DnaA-ATP molecules that are bound to the non-specific sites along the chromosome.
This model has been revisited in a study of protein-DNA interactions involving proteins with two domains connected by flexible linkers [69].
Model predictions for linking numbers and sizes of LacI-DNA loops can be tested using multiple experimental approaches, which coupled with theory could address whether proteins or DNA provide the observed flexibility of protein-DNA loops.
As protein concentration increases, the amount of free DNA drops,the electrophoretic mobility of protein-DNA complex also declines.
DOI: http://dx.doi.org/10.7554/eLife.03348.018 > -wrap-foot> To derive the structures of the intermediates observed in our experiments, we fit the continuous regions of the FECs using a quantitative model of the protein-DNA conjugate previously reported (Gao et al., 2012; Xi et al., 2012).
Several papers included in this supplement demonstrated that these elements can be more accurately predicted by integrating heterogeneous NGS data types such as DNA methylation data, histone modification marks and DNase I hypersensitivity sites, and by incorporating more accurate biophysical models of the protein-DNA interaction.
The best fitting model of protein and DNA evolution were obtained based on the AIC Akaike Information Criterionn) using ProtTest 2.4 server [ 31] and jModelTest v. 2 [ 32], respectively.
