Threading DNA

[Dilip]

I wonder if it's possible using 3DNA to superpose a given(input) DNA sequence to the conformation of the DNA in the known protein-DNA complexes from the PDB database.

[xiangjun]

I wonder if it's possible using 3DNA to superpose a given(input) DNA sequence to the conformation of the DNA in the known protein-DNA complexes from the PDB database.

The short answer is no: 3DNA does not have such functionality built in. However, 3DNA is a tool set that could be used for such purpose. For an example, have a look http://www.ncbi.nlm.nih.gov/pubmed/19289051.

Xiang-Jun