protein binding sites

Question

[yueli7]

Hello,

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

For example:

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

[Ram]

Are there any databases that contain this information? How did you get the information on AP1, for instance?

[yueli7]

Hello, RamRS,

Thank you for your reply!

It comes from Wikipedia.

AP-1 Binding Site From Wikipedia, the free encyclopedia Jump to navigationJump to search 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.

Thank you again!

Best,

Yue

[Ram]

Wikipedia is not a good primary source of information. Can you find a database that has this entry? Unless there's a database (or journal articles open to full text crawling + NLP), collecting this data will need to be manual.

[natasha.sernova]

There are a lot of similar posts in 'Bioostars.org'.

See the right panel of your own question and choose what exactly you need:

Protein Dna Binding

Is There A Database Of Known Dna Binding Proteins?

For transcription factors, for example:

How To Obtain Encode Tfbs Using The Ucsc Genome Browser

Sequence -> putative DNA binding proteins Database

Transcription Factor Dna-Binding Sites

DNA-binding sites to proteins in bacteria

etc...