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Questions and answers => General discussions (Q&As) => Topic started by: mikeshelk on October 30, 2010, 04:17:28 pm

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Title: Rebuild from sugar-phosphate backbone
Post by: mikeshelk on October 30, 2010, 04:17:28 pm

Hello, dear Xiang-Jun!

As far as I understood, "rebuild" builds structure from base parameters. So you wrote in your blog "The structural parameters can be used to rebuild the structure, which is virtually identical in base geometry (i.e., without taking consideration of the sugar-phosphate backbone) to the original structure"
Tell me please, is it possible somehow to rebuild structure using only sequence and sugar-phosphate backbone parameters? I.e. without time-consuming minimization to define approximately Calladine parameters for each nucleotide pair of a given sequence, having only backbone?

Thanks,
Mikhail Schelkunov

Title: Re: Rebuild from sugar-phosphate backbone
Post by: xiangjun on October 30, 2010, 08:56:41 pm

Quote

As far as I understood, "rebuild" builds structure from base parameters. So you wrote in your blog "The structural parameters can be used to rebuild the structure, which is virtually identical in base geometry (i.e., without taking consideration of the sugar-phosphate backbone) to the original structure"

Yes, as shown in Table 3 of the 2003 3DNA NAR papers (http://http://nar.oxfordjournals.org/content/31/17/5108/T3.expansion.html), and the corresponding examples in the directory [mono:3i9kwmym]$X3DNA/examples/analyze_rebuild/[/mono:3i9kwmym].

Quote

Tell me please, is it possible somehow to rebuild structure using only sequence and sugar-phosphate backbone parameters? I.e. without time-consuming minimization to define approximately Calladine parameters for each nucleotide pair of a given sequence, having only backbone?

No, as far as 3DNA is concerned. Also, what do you mean exactly by "sugar-phosphate backbone parameters"?
[hr:3i9kwmym][/hr:3i9kwmym]
Please note that the 3DNA [mono:3i9kwmym]analyze/rebuild[/mono:3i9kwmym] pair is purely geometry-based, without any "time-consuming minimization" involved. Building a DNA structure with or without the sugar-phosphate backbone should be (virtually) equally efficient.

HTH,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University