Rebuild DNA from C trace

[Damien]

Dear Xiang-Jun,

I have a PDB file of a DNA portion. It only contains the carbon trace (the C4 atoms). I would like to know whether it is possible to rebuild the whole structure from this trace with 3DNA? If not, do you know a way to do so?

Many thanks for your help

Damien

[xiangjun]

Hi Damien,

Thanks for posting at the 3DNA forum. Unfortunately, 3DNA (in its current version) cannot rebuild a whole DNA structure from only C4 trace. Off the top of my head, I am not sure of another tool that can perform the task either :oops:. You may have a look of NAB from David Case's lab.

Hope you would post back how it goes, possibly with more background information. Whenever possible, I am always interested in improving 3DNA in ways that make sense to me and helpful to the community.

Xiang-Jun

[Damien]

Hi Xiang-Jun

Many thanks for your answer.

One of my colleague just sent me the whole structure rebuilt from the C-trace I provided. He used Yasara. I do not still know how he did, I should receive the modeling protocol today.

Just a word of context:

I use 3D app like 3DS Max or Blender to add a straight DNA portion to macromolecular complexes made of several proteins. The DNA is deformed to bind to the known binding sites. I only use the C-trace because it reduces the number of atoms and allows real-time deformation. When I have the protein complex with the DNA, I can export in the PDB format, the PDB file containing the protein coordinates but only the trace of DNA C-atoms. Then, with the whole rebuilt DNA, it is possible to refine the structure using approaches like MD.

Damien

[xiangjun]

Dear Damien,

Thanks so much for sharing your story, and I am glad to know that your problem has been solved with  YASARA. I heard of YASARA before, but did not know that it can be used to build a whole DNA structure with only C trace.

Your question inspired me to think a bit more about the DNA modeling issue starting from a partial C or P trace. I sense the solution must be approximate, and not unique. If I have the luxury to devote more effort to 3DNA than my spare time could afford, I may come up with a geometry-based command-line-driven tool. Of course, if YASARA has solved this problem well enough, why bother to recreate the wheel.

Good luck with your project.

Xiang-Jun

[Damien]

Hi Xiang-Jun,

Commercial Yasara can perform the rebuild but it is not straightforward. I have not received the protocol yet but it needed to write a script, so to be quite quite familiar with it.

I strongly think that a rebuilding tool in 3DNA would be very useful.

Damien