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RNA structures (DSSR) / Re: Odd output for G-quadruplex structure
« Last post by xiangjun on September 20, 2017, 06:31:49 pm »
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Hi, for the structure 2chj, http://www.rcsb.org/pdb/explore/explore.do?structureId=2chj, DSSR produces some odd output.

I understand what you meant. The helix/stem/loop/ss-fragment definitions, as described in the 2015 DSSR paper in NAR, follow the literature on RNA secondary structure which is based on canonical base pairs (WC and G-U wobble). From my experience, the community is not necessarily consistent with its nomenclature/definition (if any), on the basics of (double) helix/stem/arm/paired-region/loop/pseudoknot and coaxial stacking.

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First, it identifies two helices instead of one. This is somewhat understandable since removing two strands would still produce a helical structure, but it would be nice if DSSR could identify higher-order helices automatically. Perhaps the definition of a base-pair could be generalized to include any number of nucleotides, and helices could be defined based on the stacking of these generalized base-pairs.

As you noticed, DSSR identifies two helices from a G-quadruplex structure, which clearly looks odd for this well-known structure type. This is just how DSSR works on general RNA/DNA structures where duplexes are the most frequent. Higher-level structures are case-specific: for example, G-quadruplex and i-motif are all composed of 4 strands, even though they are obviously different.

As of v1.6.1-2016aug22, DSSR already can detect and characterize i-motifs (see the DSSR User Manual). For a G-quadruplex structure (e.g. 2chj), did you notice the section "List of 4 G-quartets" as shown below:

Code: [Select]
List of 4 G-quartets
   1 nts=4 GGGG A.DG2,B.DG8,C.DG14,D.DG20
   2 nts=4 gggg A.LCG3,B.LCG9,C.LCG15,D.LCG21
   3 nts=4 GGGG A.DG4,B.DG10,C.DG16,D.DG22
   4 nts=4 gggg A.LCG5,B.LCG11,C.LCG17,D.LCG23

Is the above info useful? What more do you need? DSSR can potentially separate the four strands, and characterize the loops and directionality between the strands (as for i-motif).

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Second, it identifies each strand as a single-stranded segment, which is clearly a bug. Not sure how a single-stranded segment is defined, but I'm guessing it has to do with there being no first order base pairs (i.e. one to one base pair) in the structure.

You may call DSSR's list of single-stranded segments as "clearly a bug", from your own perspective for a G-quadruplex structure. Nevertheless, the output of DSSR follows the conventions largely adopted by the RNA (secondary) structure community. To the extent, of course, I understand and can put them into a self-consistent software program.

As I see it, your concerns about DSSR (in general) can be addressed by further its characterizations of G-quadruplex specific features, as it already does for i-motif. No size fits all. DSSR has been designed to work for the most common cases (by default), but can be quickly tailored for specified needs on a case-by-case basis. Browsing the Forum, you'll find several such cases.

HTH,

Xiang-Jun
2
RNA structures (DSSR) / Odd output for G-quadruplex structure
« Last post by jms89 on September 20, 2017, 02:50:41 pm »
Hi, for the structure 2chj, http://www.rcsb.org/pdb/explore/explore.do?structureId=2chj, DSSR produces some odd output.

First, it identifies two helices instead of one. This is somewhat understandable since removing two strands would still produce a helical structure, but it would be nice if DSSR could identify higher-order helices automatically. Perhaps the definition of a base-pair could be generalized to include any number of nucleotides, and helices could be defined based on the stacking of these generalized base-pairs.

Second, it identifies each strand as a single-stranded segment, which is clearly a bug. Not sure how a single-stranded segment is defined, but I'm guessing it has to do with there being no first order base pairs (i.e. one to one base pair) in the structure.

3
MD simulations / Re: How to analyze helical parameters of DNA with unnatural bases
« Last post by xiangjun on September 18, 2017, 10:38:50 pm »
Hi Xiehuang,

I've had a look of your attached PDB files. DX/DY/DZ deviate too much from normal purines in terms of base orientation and atoms nomenclature, as shown in the attached image for DX. They are no longer recognized as nucleotides so "find_pair" cannot identify any pairs associated with them. This is clearly a limitation of 3DNA.

Xiang-Jun
4
MD simulations / How to analyze helical parameters of DNA with unnatural bases
« Last post by shengxiehuang on September 18, 2017, 09:31:20 am »
Dear Mr Lu,
  Recently, we are trying to use the 3DNA to analyze helical parameters in our DNA MD simulations. However, base pairs DX:DA / DY:DA / DZ:DA can’t be recoganized when I used “find_pair”. Notably, the unrecoganized base-pair (named DX, DY, DZ, DA) are not typical purine or pyrimidine. How can I analysis the conformation parameters with 3DNA in a such case. 
  The pdb files of DX, DY, DZ, DA and a frame of MD simulations are given in the attachment . Thank you very much!

Best wishes!

Xiehuang Sheng
5
RNA structures (DSSR) / Re: Definition of Helix Form
« Last post by xiangjun on September 15, 2017, 11:27:50 pm »
Hi Honglue,

Thanks for your continued interest in DSSR's classifications of A-, B- and Z-helical forms. There are actually many such details in DSSR which I take as 'experimental' and are not published in the 2015 NAR paper or documented in the user manual.  Some of them will certainly end up in new publications, but no timelines.

As for DSSR reported helical forms, do they make sense? Or did you notice anything peculiar? I'd welcome your feedback.

Xiang-Jun

PS. I attended your advisor seminar (very informative) early this month at Rutgers. I saw your name in his acknowledgment list...
6
RNA structures (DSSR) / Re: Groove width distance in DSSR
« Last post by xiangjun on September 15, 2017, 08:43:33 pm »
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I just want to kindly make sure that the output groove_widths in the json file should be [minor_groove_width, minor_groove_width_refined, major_groove_width, major_groove_width_refined], not [minor_groove_width, major_groove_width,, minor_groove_width_refined, major_groove_width_refined], right?

You're right. The four numbers are minor groove width (raw and refined) and major groove width (raw and refined), as in the listing of 3DNA analyze output.

Xiang-Jun
7
RNA structures (DSSR) / Re: Definition of Helix Form
« Last post by lvelve0901 on September 15, 2017, 05:03:35 pm »
Hi Xiangjun,

Could you please tell me when you will report the detail of helix form definition in dssr? My advisor asked me some questions in terms of how dssr identify helix form so I would like to know more details of this.

This is not urgent so please take your time.

Thank you so much.

Best,
Honglue
8
RNA structures (DSSR) / Re: Groove width distance in DSSR
« Last post by lvelve0901 on September 15, 2017, 05:00:36 pm »
Hi Honglue,

I've finally added groove widths into DSSR JSON output, per your request. Now with --more, you will see the groove_widths key in helices/stems output. The corresponding value is an array with 4 numbers: [minor_groove_width, major_groove_width, minor_groove_width_refined, major_groove_width_refined], as they appear in the 3DNA analyze output. For example, "groove_widths":[12.023,11.942,17.338,17.281] for the 4th dinucleotide step in 355d.

As mentioned in my previous responses, some additional features from the 3DNA analyze program have been implemented into DSSR. They will be revealed later.

Please have try and report back how it goes. Note I've not updated the release version on the download page yet. However, the download files have been updated.

Best regards,

Xiang-Jun


Hi Xiangjum,

I just want to kindly make sure that the output groove_widths in the json file should be [minor_groove_width, minor_groove_width_refined, major_groove_width, major_groove_width_refined], not [minor_groove_width, major_groove_width,, minor_groove_width_refined, major_groove_width_refined], right?

Best,
Honglue
9
General discussions (Q&As) / Re: Single Stranded DNA
« Last post by xiangjun on September 14, 2017, 12:46:58 pm »
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is there a software suitable for single stranded DNA structure modelling

This is a vague question, and I'm not sure how to answer it. Did you know the NAB tool from the David Case laboratory at Rutgers? NAB is a flexible "molecular manipulation language" designed for the "Generation of Models for 'Unusual' DNA and RNA". In principle, NAB in combination with AMBER should do the trick.

As far as 3DNA/DSSR goes, the "fiber" program can generate arbitrary linear double or single-stranded DNA models. The other two programs, "rebuild" and "mutate_bases", can also be applied to certain aspects of modeling studies (see my blogpost "The 3DNA mutate_bases program is cited in Nature").

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... Could that be a workable solution?

What you said make sense, in general. However, only doing it will reveal concrete caveats and possible solutions. Please post back if you think 3DNA/DSSR may be of some help along the way, and I'll try my best to help.

As a side note, you may already know "RNA-Puzzles", and the numerous tools available for RNA modeling.

Best regards,

Xiang-Jun

 
10
General discussions (Q&As) / Single Stranded DNA
« Last post by aribis77 on September 13, 2017, 08:12:10 am »
A very common query amongst Nucleic acid structural biologists or rather modelling community is that is there a software suitable for single stranded DNA structure modelling. I would like to ask the same here if this software can do the same. If not would first designing the double stranded regions (stem) and then joining them with linear strands separated from double stranded modelling options and then simulating the whole joined structure make sense. I know that separating linear starnds from double stranded structures can be painstaking as that would mean reassignment of charges. But what is this is done on a linear double stranded structure so atleast the problems of conformational bends does not come into the picture. Then finally let the whole structure  ( ss linear regions joined with ds modelled regions) fold within a simulation. Could that be a workable solution?
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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.