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Are there any computational tools to predict the binding affinity to specific DNA motifs from protein domain sequence information?

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up vote 3 down vote accepted

Those that come up from a Google search ("predict DNA binding from protein domain tool") seem pretty well suited to your question.

Depending on your computational/statistical know-how you might also find these papers relevant

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The OP is not asking to find which residues interact with DNA, but which DNA motifs are preferred by a given binding protein. – Erik Garrison Feb 18 '13 at 19:24

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