I am trying to study docking of drug-DNA interaction and for that I need PDB file.

How can I get a pdb file for my custom dsDNA sequence (10-11 base pairs long)?

I will really appreciate if you can please guide me.

Thank you all for your time.

  • 1
    $\begingroup$ Pymol can build nucleic acids and is free for students. $\endgroup$
    – canadianer
    Sep 9, 2021 at 15:23
  • $\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$
    – Community Bot
    Sep 9, 2021 at 16:12
  • $\begingroup$ Further to @canadianer here ins a link that looks as if it might be helpful pymolwiki.org/index.php/Builder . $\endgroup$
    – David
    Sep 11, 2021 at 16:47

1 Answer 1


UCSF Chimera is free to use and is very versatile for molecular modeling. It has a Build Structure module (found in Tools->Structure Editing) useful for building proteins or nucleic acid sequences (selections in the left pane).

Here I inserted the sequence

Clicking Apply performs the build.

3D rendering

It is then saved with File->Save PDB. Note: the structure is devoid of hydrogen ions, which can be added using Tools->Structure Editing->AddH. I have always used this program because its outputs are readily accepted by CHARMM-GUI (the server adds the hydrogen ions in this case).


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