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Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that theoretical models describe the macromolecular interaction energetics accurately. While several methods have been proposed, there has not been a careful comparison of how well the different methods are able to predict biologically important quantities such as thedoi:10.1093/nar/gkl1103 pmid:17259221 pmcid:PMC1851630 fatcat:h7jf3qqzfjgzfjco2jr4tjrfdy