Protein Bound DNA via w3DNA

[acolasanti]

This question arrived via email :

I have a question regarding the reconstruction of a protein-bound DNA model from Web 3DNA.
When I use this function to create a complex of a protein bound to a DNA duplex, is the DNA structure (and the protein structure) locally distorted by the interaction?

[acolasanti]

When using the reconstruction section of the w3DNA website to create protein bound DNA the following method applies

-  DNA base pairs interacting with protein in the original X-ray will adopt the same configuration (pair and step parameters) as those found in the original structure.  Because of this the model must have at a minimum the same number of steps as found in the X-ray structure.

- Extra DNA that you add to the beginning or end of the structure will adopt the configuration (A-, B-) selected on the w3DNA site.

If I did not answer your question please let me know so that I can further assist you.

Thanks,

Andrew