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Questions and answers => General discussions (Q&As) => Topic started by: Nutch [Bot] on September 24, 2007, 03:52:09 am

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Title: Zp/ZpH and depth of DNA
Post by: Nutch [Bot] on September 24, 2007, 03:52:09 am

I'm a new user of 3DNA and I have two questions about the following parameters:
 
1) Zp/ZpH: Could you tell me how are they calculated? I can't find any reference about it.

2) Is there a way to calculate the depth of minor/major grooves of DNA from 3DNA? Is there a clear definition of groove depth?

Thanks a lot...

Guillaume

Title:
Post by: xiangjun on September 24, 2007, 09:40:06 pm

Thanks for using 3DNA!

Please refer to Lu et al A-DNA paper (J. Mol. Biol. 300, 819-840, 2000) (http://http://rutchem.rutgers.edu/~xiangjun/3DNA/ADNA_citations.html) on the definition of Zp. ZpH is similarly defined, but w.r.t. to the middle helical frame.

3DNA does not provide groove depth info (yet). Please refer to Curves (http://http://www.ibpc.fr/UPR9080/Curindex.html) for it. Also note the "-c" option of "find_pair" in 3DNA to generate input to Curves directly from a PDB file.

In the meantime, if you or anyone know of "a clear definition of groove depth", or better yet, with implementation, please do let me know. I am interested in adding groove depth parameters in future 3DNA release.

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