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Questions and answers => w3DNA -- web interface to 3DNA => Topic started by: sowmya on November 16, 2022, 06:33:32 am

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Title: Cannot understand what a base pair type means from web-3DNA output
Post by: sowmya on November 16, 2022, 06:33:32 am

Dear Dr. Xiang,

I was analyzing the base pair type distribution among a dataset of RNAs that I have collected for my study using the pair.csv file for those PDB IDs obtained using web-3DNA. When I compiled the list of unique base pair types I noticed certain base pairs with a P, which are: P+A, A-P, P-G, P+G, C-P and P-A.
I got information on the other base pair types from the x3DNA website: http://x3dna.org/highlights/named-base-pairs, but I'm unable to find information on the above mentioned base pairs. Can you share some resources to understand what these named base pairs mean and how they are identified (in terms of the structural orientation of the bases and other parameters)?

Thank you
- Sowmya

Title: Re: Cannot understand what a base pair type means from web-3DNA output
Post by: xiangjun on December 25, 2022, 11:33:44 am

See the paper "DSSR: an integrated software tool for dissecting the spatial structure of RNA" (https://doi.org/10.1093/nar/gkv716).

Quote

Identification of nucleotides

        Note that pseudouridine (PSU) is shortened to ‘P’, due to its special C1′–C5 glycosidic link- age (Figure 2).

The M–N versus M+N relative base orientations

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