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The first problem is addressed in this contribution. There have been very successful attempts of this approach, including Monte Carlo approaches [44–46], but these are only valid for not too large systems. The second problem is the focus of a recent publication of our group [47]. In summary, [47] proposes a compromise between providing a good description of the protein-DNA binding free energy and allowing for the exploitation of homology information. This gives a robust effective energy (i.e. the effective energy of the homology built complex is the same as that of the native complex).

C. Kullback and colleagues have recently developed a theoretical formalism to estimate the relevance of differences in the protein-DNA and DNA-DNA binding free energies [48]. This formalism links the thermodynamics of biomolecular interactions and the statistical mechanics of binary systems. We have implemented this approach in the software package “ProteinDNADesign”, which provides an estimate of the relative protein-DNA binding free energy based on the physicochemical properties of the protein and the DNA.

The main idea of the compromise is to use a PEEF for protein-DNA binding and a simpler PEEF for DNA-DNA interaction. The latter PEEF is derived from a PEEF model of protein-DNA binding. The biological PEEF (used here as starting point for the physical PEEF) is a simple PEEF which does not contain sequence-dependent parameters. In order to build the DNA-DNA PEEF, an entropic penalty term is added to the PEEF of protein-DNA binding. This penalty term is constructed in such a way that the DNA-DNA PEEF obeys a simple statistical mechanics, i.e., it is zero when two DNA molecules are unbound and the total number of bound DNA molecules is either one or two. It is shown that the weighted sum of the free energy in the biological PEEF and the penalty term in the DNA-DNA PEEF provides a reasonable estimate of the free energy of the protein-DNA binding free energy.

Now, that doesn't mean fanart is legal in Japan, and it doesn't mean that someone who subbed the original Japanese dub of an anime isn't copying someone else's work. But I don't think that it's OK to distribute someone else's work and claim it as your own. As much as some people hate the idea of fansubs, it's still legal - and it's not something I'm willing to go after. 827ec27edc