Show Posts
1
General discussions (Q&As) / Using base pair parameters calculated with CompDNA and 3DNA for reconstruction
« on: June 24, 2015, 04:03:11 pm »
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
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