How can I predict DNA binding affinities from a protein sequence?

Question

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

Answer 1

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

• BindN
• DNAbinder

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

• Huang et al, Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties
• Gao et al, A threading-based method for the prediction of DNA-binding proteins with application to the human genome