Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations -- J Comput Biol.

structure and covariation angle looks interesting

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http://www.liebertonline.com/doi/abs/10.1089/cmb.2006.13.929
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16761919&query_hl=1&itool=pubmed_docsum
J Comput Biol. 2006 May;13(4):929-45.
Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations.
Gunewardena S, Jeavons P, Zhang Z.