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Questions and answers => RNA structures (DSSR) => Topic started by: miaobeibei925 on January 21, 2021, 04:07:02 pm

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Title: composite DNA template length
Post by: miaobeibei925 on January 21, 2021, 04:07:02 pm
Dear Xiangjun,

I am trying to use the composite function on w3DNA 2.0 to generate a DNA-protein complex with the 1KX5 pdb.
The binding information page shows the DNA Template length is 146bp. However, the length of the 1kx5 DNA is 147bps. I downloaded the resulting composite pdb file and the DNA sequence in the composite model is different from that I entered. (DNA chain A residues 165 to 185 are different).

What can I do to change the DNA in this composite model to the DNA I entered?

Thank you
Title: Re: composite DNA template length
Post by: xiangjun on January 21, 2021, 09:46:41 pm
Hi,

Thanks for your question on the Composite module in Web 3DNA 2.0. Composite is an advanced feature that mades use various 3DNA programs and ad hoc scripts. Other than the general idea, I honestly do not know how things work in details. Right now, I have no time to dig things up either. In the long run, I may consider to consolidate all these steps into a DSSR module to automate the process.

Shuxiang, the developer of Web 3DNA 2.0 but no longer involved in the project, may chime in with some insights.

Xiang-Jun

 
Title: Re: composite DNA template length
Post by: xiangjun on February 11, 2021, 04:46:42 pm
Hi,

I have created a brand-new program for template-based modeling of nucleic acid structures, including DNA-protein complexes. Now users can easily specify their own templates via the command-line. Using your 1kx5 as an example, one can easily build the attached model. See also two more complexes models.

This novel modeling program is distributed as a module of DSSR Pro. (http://innovation.columbia.edu/technologies/CU20391)

Best regards,

Xiang-Jun

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.