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Questions and answers => General discussions (Q&As) => Topic started by: Dilip on June 22, 2009, 01:20:48 pm

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Title: Threading DNA
Post by: Dilip on June 22, 2009, 01:20:48 pm

I wonder if it's possible using 3DNA to superpose a given(input) DNA sequence to the conformation of the DNA in the known protein-DNA complexes from the PDB database.

Title: Re: Threading DNA
Post by: xiangjun on June 22, 2009, 10:17:58 pm

Quote from: "Dilip"

I wonder if it's possible using 3DNA to superpose a given(input) DNA sequence to the conformation of the DNA in the known protein-DNA complexes from the PDB database.

The short answer is no: 3DNA does not have such functionality built in. However, 3DNA is a tool set that could be used for such purpose. For an example, have a look http://www.ncbi.nlm.nih.gov/pubmed/19289051 (http://www.ncbi.nlm.nih.gov/pubmed/19289051).

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