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Questions and answers => RNA structures (DSSR) => Topic started by: jctoledo on March 26, 2013, 11:19:15 am

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Title: DSSR output - Base pair characteristics
Post by: jctoledo on March 26, 2013, 11:19:15 am
Hi all,

Loving DSSR for analyzing RNA structures! I was wondering what are all the qualitative parameters about base pairs that are captured by this tool are. For example I ran DSSR on PDBID 3OXO the and following (abridged) sample base pair details are given:

Code: [Select]
3 A.C3             A.G86            [C-G] WC           19-XIX    cWW cW-W
...
8 A.G7             B.A64            [G+A] Linker       00-n/a    tSS tm+m
...
9 A.G8             A.A81            [G-A]              00-n/a    tSH tm-M
...
22 A.G32            A.A71            [G+A]              00-n/a    cH. cM+.


Where for the case of base pair #3, I have recognized the following annotations:
- "3": Base pair number
- "A.C3": Chain 1, residue identifier 1, residue position 1
- "A.G86": Chain 2, residue identifier 2, residue position 2
- "[C-G] WC": A descriptive label for this base pair
- "19-XIX": The Saenger class for this base pair (00-n/a when not available)
- "cWW": The Leontis-Westhof nomenclature for interacting edges (cis Watson-Crick/Watson-Crick -> Class #1)

However what does the last column refer to? For example:
Base pair #3: "cW-W"
Base pair #8: "tm+m"
Base pair #9: "tm-M"
Base pair #22: "cM+."

Also, what does the "." signify when found in either of the last two columns of this output?

Regards,
Jose
Title: Re: DSSR output - Base pair characteristics
Post by: xiangjun on March 26, 2013, 01:33:06 pm
Hi Jose,

Thanks for trying out DSSR and for your kind comment about the program. User feedback like yours is a great incentive for me to make DSSR a better tool to serve the RNA structure community.

To start with, I have tried hard to made DSSR easy to set up and play with. Based on my reading of literature in structural biology, I've made the DSSR output more intuitive (compared to previous 3DNA programs). For example, A.U2647 means U2647 on chain A. So far, I have not heard of any installation problem yet, and I am glad that you can make sense of most items in the DSSR output.

Your question regarding the meaning of the last column is well expected. It represents my own notation to specify a base pair, as elaborated below:

HTH,

Xiang-Jun

PS. Does "PDBID 3OXO" correspond to an RNA structure?
Title: Re: DSSR output - Base pair characteristics
Post by: jctoledo on March 26, 2013, 01:56:53 pm
Thank you for the prompt response. This cleared things up!

FYI, I had a typo in my original post. The basepairs were extracted from PDBID: 3OX0 [http://www.rcsb.org/pdb/explore.do?structureId=3OX0] (got my O's and 0's confused)

Jose

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.