Are there some in silico methods or tools by which the nucleotides important for DNA -protein interaction can be found?
I have some promoters which binds to a response regulator, I wanted to know to which nucleotides, my protein is recognising for binding.
you would more likely search for tools to find transcription factors binding sites on upstream regions which is one of the core problems of bioinformatics
you'd better try TRANSFAC/jasper databases
Contra web server
PROMO database
Thank you Tarek for your suggestions but I am working in the bacterial system and all these databases deals with Eukaryotes. So they are of not much help to me.
then try
CollecTF
regulonDB
http://pepper.molgenrug.nl/
http://bioinfo.ucc.ie/TFbsST/
http://www.prodoric.de/
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