protein dna binding sites

yueli · 08-04-2019, 10:40 AM

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 · 08-04-2019, 11:24 AM

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 · 08-04-2019, 11:36 AM

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 · 08-27-2019, 11:04 PM

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 · 08-28-2019, 05:13 AM

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 · 08-04-2020, 02:51 AM

Thank you so much for your replying.

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08-04-2019, 10:40 AM	#1
yueli Member Location: china Join Date: May 2013 Posts: 71	protein dna binding sites 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

08-04-2019, 11:24 AM	#2
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 523	Are these proteins DNA-binding proteins, or are you wanting to find which DNA-binding proteins bind to the gene region of these proteins? __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

08-27-2019, 11:04 PM	#4
SapirP Junior Member Location: Israel Join Date: Aug 2019 Posts: 3	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 Last edited by SapirP; 09-04-2019 at 05:57 AM.

08-04-2019, 11:36 AM	#3
yueli Member Location: china Join Date: May 2013 Posts: 71	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

08-28-2019, 05:13 AM	#5
yueli Member Location: china Join Date: May 2013 Posts: 71	Hello, SapirP, Thank you so much for your answer. Thank you for the clue you give to me. Thank you again! With Best, Yue

08-04-2020, 02:51 AM	#6
arjeet45o Junior Member Location: ludhiana Join Date: Aug 2020 Posts: 2	Thank you so much for your replying.