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Author Topic: How to look for abasic site using DSSR  (Read 116 times)

Offline lvelve0901

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How to look for abasic site using DSSR
« on: April 26, 2017, 12:50:57 pm »
Hi Xiangjun,

Long time no contact. I hope you had a good time recently.

I have a question about DSSR. Can DSSR detect abasic site?

For example, in 1l2c.pdb and 1l2d.pdb, there is a abasic site HPD18DG7. I thought this could be written in internal loop; however, the internal loop only detect a lower base pair open (DA23DT2).

Best,
Honglue

Offline xiangjun

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Re: How to look for abasic site using DSSR
« Reply #1 on: April 26, 2017, 01:56:41 pm »
Hi Honglue,

As shown in Fig.1 (see below) of the DSSR paper, "Nucleotides are recognized using standard atom names and base planarity." Since abasic sites (e.g., HPD18 in chain C of PDB id 1l2c) do not have proper base atoms, they are not recognized as nucleotides by DSSR to begin with. Naturally, they do not appear in later analysis results of DSSR output. This is just the way DSSR works and you may take it as a deficiency. Please let me know if you have a better way to handle such cases.



Hope this clarifies your confusions.

Xiang-Jun
« Last Edit: April 26, 2017, 02:15:05 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

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Re: How to look for abasic site using DSSR
« Reply #2 on: April 26, 2017, 03:23:57 pm »
Does that mean DSSR cannot detect abasic site, since there is no base atom?

Thanks.

Best,
Honglue

Offline xiangjun

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Re: How to look for abasic site using DSSR
« Reply #3 on: May 01, 2017, 11:35:39 pm »
Hi Honglue,

I've added an option --abasic to DSSR to take abasic sites as nucleotides, as long as main-chain backbone atoms are preserved: P, O5', C5', C4', C3', and O3'. Quick tests on 1l2c and 1l2d show that this new DSSR feature is working as designed (e.g., C.HPD18 is listed in an internal loop). Understandably, the abasic nucleotides won't be involved in base pairing and stacking interactions.

The DSSR on the download page (still labeled v1.6.8-2017mar28) has been updated. Have a try and report back if it solves your problem.

Xiang-Jun
« Last Edit: May 01, 2017, 11:37:57 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.