DNA methylation is known to affect the interactions with DNA-binding proteins, although detailed molecular insights of how cytosine methylation interferes with binding events are only known yet for very few DNA binding proteins. DNA methylation can affect direct contacts of proteins with the major groove, affect interactions with the minor groove through DNA structural changes, or alter the chromatin structure. Since only a small number of structures of DNA targets and protein-DNA complexes with cytosine methylation are available in the Protein Data Bank, we developed methyl-DNAshape that uses the mining of all-atom Monte Carlo simulations to predict the effect of cytosine methylation on the DNA shape features minor groove width (MGW), Roll, propeller twist (ProT), and helix twist (HelT) in comparison to the prediction of those features in unmethylated DNA using DNAshape.

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