Tool to predict protein binding to DNA (what exact nitrogenous bases)

Question

[Rafael Soler]

Hi!

Do you know any tool that predicts in which DNA sequence a certain amino acid sequence would bind?

For example, I have an amino acid sequence "MKWKHVPFLV" that has been computationally predicted for me to bind to DNA. Can you know exactly what bases binds to (ATTTGACA...)?

Thanks!

Answer 1

[Mensur Dlakic]

As a general rule, there is no simple protein-DNA binding code with one-to-one correspondence between protein and DNA residues. There are exceptions: for zinc-finger transcription factors and TAL effectors one can predict what DNA they will bind by knowing the protein sequence. For most proteins, however, this is either impossible or can be done only sporadically.

[Rafael Soler]

Thank you!