3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: Charu on July 24, 2012, 10:14:13 am

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Title: Analysis_assumptions!
Post by: Charu on July 24, 2012, 10:14:13 am

Hi,

I am doing structure analysis for 3DFV which is GATA3-DNA complex structure. I wanted to ask that the assumption that mutating the bases using mutate_bases will show us the structural and binding differences that the protein GATA3 might have with respect to bases, is it correct?

because as i've been analysing, i've found almost all the same bonds and very little change in binding preferences of bases and bond lengths. I'm analysing using PyMOL.

Thanks.

Title: Re: Analysis_assumptions!
Post by: xiangjun on July 24, 2012, 02:41:05 pm

The 3DNA program mutate_bases does exactly as its name suggests, i.e., mutate DNA/RNA bases, and from a pure geometric approach. It is up to the user (with any other desirable tools) to make sense of "structural and binding differences" between mutated and native structures.

Xiang-Jun

Title: Re: Analysis_assumptions!
Post by: Charu on August 02, 2012, 04:20:38 am

Thank you so much.

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.