3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: luhong on November 23, 2009, 08:05:45 pm

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.2 (DSSR Manual) · Homepage

Title: Deformability of a small DNA fragment
Post by: luhong 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 (http://rutchem.rutgers.edu/~olson/ave_dpn.html)

Thank you!

HongLu

Title: Re: Deformability of a small DNA fragment
Post by: xiangjun 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 (http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=4&t=108)" 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

Title: Re: Deformability of a small DNA fragment
Post by: luhong on November 24, 2009, 12:57:29 am

It's very helpful for me. Thank you.

Hong

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