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Questions and answers => General discussions (Q&As) => Topic started by: sammeyer on November 05, 2012, 11:24:33 am

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Title: DNA elastic parameters from NDB database
Post by: sammeyer on November 05, 2012, 11:24:33 am

Dear users

I am looking for elastic parameters for the DNA bp-step deformations : equilibrium values and stiffness matrices.
These values were first published in [Olson, 1998]. In a more recent paper, [Balasubramanian, 2009], new values were obtained with a larger database. However, not all parameters are visible in the paper (not the cross-terms of the matrix).
Are these values included in 3dna ? I can't find them on the NDB website ?

Thanks for help

Sam Meyer

Title: Re: DNA elastic parameters from NDB database
Post by: xiangjun on November 05, 2012, 11:32:27 am

No, these new values are not included in 3DNA. You're advised to contact the authors of the 2009 Balasubramanian paper for further details.

For those who are interested in the original Olson et al. 1998 dataset, please check the post "Some details on PNAS98 DNA sequence-dependent deformability (http://forum.x3dna.org/related-topics/some-details-on-pnas98-dna-sequence-dependent-deformability/)".

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