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Author Topic: Deformability of a small DNA fragment  (Read 15527 times)

Offline luhong

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Deformability of a small DNA fragment
« on: November 23, 2009, 08:05:45 pm »
I am a newbie on this field and have a question on deformability.

Suppose I have a small DNA fragment, such as "ATTGCGGATATA", how to calculate the deformability of this motif, Any formula?

Should I use the table (Part A: Protein-DNA complexes) in the following page?
http://rutchem.rutgers.edu/~olson/ave_dpn.html

Thank you!

HongLu
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Offline xiangjun

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Re: Deformability of a small DNA fragment
« Reply #1 on: November 23, 2009, 11:38:31 pm »
3DNA does not perform energy calculations per se, but please have a look of the post "deformation energy calculation program" by Dr. Thomas Gaillard at the Users' contributions section.

If you have further technical questions, you may want to post over there: I think Dr. Gaillard would follow up.

Xiang-Jun
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Offline luhong

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Re: Deformability of a small DNA fragment
« Reply #2 on: November 24, 2009, 12:57:29 am »
It's very helpful for me. Thank you.

Hong
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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