protein dna binding sites

[yueli]

Hello,

I have around 200 protein's fasta file. How can I find these proteins binding site with DNA?

For example:It comes from Wikipedia.

The AP-1 binding site, also known as the AP-1 promoter site, is a DNA sequence to which AP-1 transcription factors are able to bind. The AP-1 binding site, in humans, has a nucleotide sequence of ATGAGTCAT.

Thanks in advance!

Best,

Yue

[SNPsaurus]

Are these proteins DNA-binding proteins, or are you wanting to find which DNA-binding proteins bind to the gene region of these proteins?

[yueli]

Hello, SNPsaurus,

Thank you so much for your replying.

I want to know the DNA sequencing which can binding to the protein.

Thank you in advance for your great help!

Best,

Yue

[SapirP]

Hi Yue,

To my knowledge, there is not a certain way to find a DNA sequence that a specific protein binds (accept for an experimental approach, of course).

If there are solved structures of the 200 proteins with a strand of DNA, it is not hard to see which of the nucleotides is in contact with the protein.

However, if we stay only at sequence level, I am not sure there is a relevant prediction method, at least to my knowledge.

From sequence perspective, there are prediction tools designed to try and determine if a protein is DNA binding only based on sequence (our lab also has one- DR. PIP). A new prediction method to identify couples of proteins and the DNA they bind is currently being developed in our lab.

Good luck!
Sapir

[yueli]

Hello, SapirP,

Thank you so much for your answer.

Thank you for the clue you give to me.

Thank you again!

With Best,

Yue

[arjeet45o]

Thank you so much for your replying.