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I am a computer scientist and we are working on protein function prediction algorithms. Right now, we would like to examine protein-DNA binding properties computationaly. For this, we would make use of datasets about containing DNA-binding proteins and the DNA sequences they bind to. I was looking on Gene Ontology and Protein Databank where I'd expect such informations, but I was unable to find it. Are such data presently difficult to obtain? Or are simply not collected? Or could you give me some direction where to look for such data. Thanks.

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    $\begingroup$ Try these searches: TRANSFAC, JASPAR, ENCODE, position weight matrices (or PWMs) $\endgroup$ – mdperry Sep 2 '15 at 13:49
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You are seeking a database of transcription factor binding specificities. Some model organism databases (which are manually curated), such as Wormbase contain some of this annotation. I suggest you search PubMed for papers by Tim Hughes at the University of Toronto. He has published extensively on this topic over the past 5 years. Papers he cites, and papers that cite him, will let you bootstrap your way in to the topic.

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