Using base pair parameters calculated with CompDNA and 3DNA for reconstruction

[jbirkh]

Hello,

I am currently attempting to build an accurate sequence-specific structure of DNA for macro-molecular docking computations. I plan on using the customized base-pair-step/nucleotide parameters reconstruction capability of w3DNA to do this.

My question is whether or not it is acceptable to use average intra-base pair parameters that were calculated using 3DNA and average inter-base parameters that were calculated using CompDNA for the reconstruction.

The 2008 Nature Protocols Paper states that the reference frames of CompDNA and 3DNA are nearly similar and thus the parameters will closely resemble each other, but I am not quite sure if that is enough. The parameters that I would like to use come from [url]Olson, et al. Proc.Natl.Acad.Sci.USA, 95(19):11163–11168, 1998 and Perez et al. Nucl. Ac. Res., 32(20):6144–6151, 2004.

If anyone has any insight on this, it would be greatly appreciated.

Thanks,

jbirkh

[xiangjun]

Hi jbirkh,

Thank you for your interest in using 3DNA and posting your questions on the Forum. There are two aspects to your questions. On one hand, the rebuild command in 3DNA (also used in w3DNA) can build a 3D structure based on the sequence and associated base-pair and step parameters associated with it, no matter where the parameters come from or whether they make physical sense. So you can build a DNA model using a mixture of parameters from 3DNA and CompDNA (or anywhere else). On the other hand, it is up to the users to decide whether such combinations make 'sense' in their circumstances. Obviously, the 3DNA rebuild program assumes implicitly parameters from the analyze program. You can verify the rebuilt model by run the analyze command, and you will get exactly the parameters you started with.

HTH,

Xiang-Jun