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I want to know what kind of bonds are there between a Transcription Factor and its DNA binding site when the complex is created. This information will be used to determine the method for a molecular Dynamics simulation, which intends to predict/calculate the binding energy/Gibbs free energy.

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    $\begingroup$ You might take a look at this paper: ncbi.nlm.nih.gov/pmc/articles/PMC3425445 ("MM energy functions, on the other hand, are composed of independent, physicochemical energy terms that capture van der Waals and Coulombic interactions, solvation effects, and other atomic interaction energies") $\endgroup$ – Alex Reynolds Aug 22 at 15:57
  • $\begingroup$ Thanks for answering. I would like some more specific information but I found other useful information $\endgroup$ – Phineas Aug 22 at 16:13

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