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Author Topic: Classifying structures into A, B , AB, TA .. types  (Read 356 times)

Offline Puru@1998

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Classifying structures into A, B , AB, TA .. types
« on: June 19, 2018, 03:42:05 pm »
Hello

I have been working on RNA/DNA hybrids with conformational parameters, along with DNA and RNA duplexes.

I was wondering if there is a script , another way to classify the structures that I have compiled by A, B, AB, TA- type( which is done and seen on the forum)?


Sincerely,
Puru

Offline mauricio esguerra

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Re: Classifying structures into A, B , AB, TA .. types
« Reply #1 on: June 20, 2018, 04:10:54 am »
Hej Puru,

Perhaps a look at the original reference of Xiang-Jun Lu for 3DNA, say, Figure 5 of his 2003 paper in Nucleic Acids Research will come in handy.

http://dx.doi.org/10.1093/nar/gkg680

In that figure Inclination vs. x-displacement, Roll vs. Slide, and Zp(h) vs. Zp are plotted and are quite neat indicators of the conformational types of nucleic acids.

There's even an older 2000 paper by the same first author, and the creator or 3DNA, which predates 3DNA. It is also quite the recommended read.

http://dx.doi.org/10.1006/jmbi.2000.3690


All of the parameters needed to do the figures in the two mentioned papers are easily obtained using 3DNA.


Hope this helps,

Mauricio




Offline xiangjun

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Re: Classifying structures into A, B , AB, TA .. types
« Reply #2 on: June 20, 2018, 01:29:06 pm »
Thanks, Mauricio, for chiming in and for your nice words about my early publications.

Quote from: Puru
I was wondering if there is a script , another way to classify the structures that I have compiled by A, B, AB, TA- type( which is done and seen on the forum)?

Could you please clarify your question, preferably with a concrete example?

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Puru@1998

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Re: Classifying structures into A, B , AB, TA .. types
« Reply #3 on: June 22, 2018, 01:26:17 pm »
Hello. Thank you for your responses.

I will clarify my questions to the best of my ability.

I am trying to classify structures as A ( 75-100 percent = A , 57/58- 75 percent = A-like , 43% - 58% = A to B)  ..in this manner. I was wondering if 3dna has a way of accomplishing this without me having to do it manually say for a database of 300 structures of DNA/DNA and RNA/RNA duplexes that I have created.

Examples: step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
   1 GG/CC   -2.93    8.97    0.37   -3.31    8.93    0.93     B
   2 GT/AC   -3.35    9.11   -0.39   -4.65    9.11    0.27     B
   3 TG/CA   -2.75    8.65   -0.88    0.06    8.42   -2.19     B
   4 GC/GC   -3.75    8.88   -1.02   -4.46    8.86    1.15     B
   5 CA/TG   -2.21    8.39   -0.80    0.87    8.11   -2.24
   6 AA/TT   -3.16    8.72   -0.76   -3.15    8.69   -1.08     B
   7 AC/GT   -3.34    8.80    0.30   -4.58    8.79   -0.36     B
   8 CA/TG   -3.15    8.59    0.82   -5.42    7.85    3.62
   9 AA/TT   -3.40    8.91   -0.05   -5.18    8.77    1.57     B
  10 AA/TT   -2.85    9.21    0.49   -4.46    8.93    2.31     B
  11 AT/AT   -2.73    9.23    0.37   -5.90    8.10    4.48
  12 TT/AA   -3.06    8.49    0.75   -7.77    2.66    8.09
  13 TG/CA   -1.93    8.53   -1.20   -1.73    8.42    1.80
  14 GA/TC   -3.71    8.29   -1.70   -1.39    8.33   -1.77
  15 AT/AT   -3.33    8.91    0.01   -3.85    8.89   -0.62     B
  16 TA/TA   -3.07    8.68    0.30   -3.26    8.62   -1.09     B
  17 AA/TT   -3.23    8.99   -0.12   -3.62    8.93   -1.05     B
  18 AG/CT   -2.99    8.80   -0.12   -4.25    8.76    0.81     B
  19 GC/GC   -2.88    8.98   -0.05   -2.91    8.98   -0.13     B
  20 CA/TG    ---     ---     ---     ---     ---     ---     ---
  21 AA/TT    ---     ---     ---     ---     ---     ---     ---
  22 AT/AT   -1.31    5.67   -0.75   -1.12    5.67   -0.38
  23 TG/CA   -3.05    9.04   -0.43   -1.94    9.05   -0.15     B
  24 GC/GC   -3.22    9.12   -0.18   -3.87    9.12    0.02     B
  25 CT/AG   -3.15    8.71    0.12   -4.40    8.67    0.80     B
  26 TT/AA   -3.20    9.07   -0.14   -3.66    9.01   -1.00     B
  27 TT/AA   -3.31    9.00   -0.28   -4.03    9.00   -0.28     B
  28 TT/AA   -3.32    8.90   -0.38   -3.06    8.75   -1.69     B
  29 TT/AA   -2.84    8.83   -0.02   -2.70    8.77   -0.99     B
  30 TT/AA   -3.17    8.80   -0.39   -4.01    8.81   -0.16     B
  31 TG/CA   -2.68    8.86   -0.39   -2.17    8.73    1.56     B
  32 GG/CC   -2.62    8.93    0.55   -4.88    8.43    3.01
  33 GC/GC   -3.01    9.06    0.57   -4.46    8.93    1.66

About 63 percent B so, B- Like
Structure 1ihf.pdb



    step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
   1 Ug/gA   -0.59    1.90  -10.29   -1.26   -5.96   -8.21
   2 gg/gg   -0.03   11.87   -0.05   -0.04   11.87   -0.05
   3 gA/Ug    4.30    6.48    0.76    4.86    6.47    0.71
   4 AG/GU    ---     ---     ---     ---     ---     ---     ---
   5 GA/UG    ---     ---     ---     ---     ---     ---     ---
   6 AG/GU    ---     ---     ---     ---     ---     ---     ---
   7 GA/UG    0.91    7.95   -3.89    0.95    7.96   -3.89
   8 AU/AU    ---     ---     ---     ---     ---     ---     ---
   9 UG/GA    4.86   -3.16   -3.09    3.46   -5.61   -2.45
  10 GG/GG    2.86   -8.07    9.47    0.69  -11.79    7.22
  11 GU/UG   -0.70   -5.57    0.33   -0.39   -5.58   -0.02
  12 UA/UU    4.87    4.65    9.91    6.37    4.62    8.66
  13 Ag/gU    ---     ---     ---     ---     ---     ---     ---
  14 gU/Ag    ---     ---     ---     ---     ---     ---     ---
  15 UG/GA    4.76   -3.15   -3.07    3.40   -5.68   -2.41
  16 GU/UG   -0.69   -0.62    3.16    3.87    0.05   -5.38
  17 UG/GU   -1.13    9.00   12.68   -1.60    9.15   12.56
  18 GU/UG   -2.66    2.33    7.98   -3.11   -1.49    5.97
  19 UA/UU    1.44    7.36    8.41    1.48    7.36    8.39
  20 Ag/gU    ---     ---     ---     ---     ---     ---     ---
  21 gG/Gg   -1.88   -0.50    6.72   -3.52   -0.95    6.73
  22 GG/GG    2.93   -8.32    9.69    0.64  -11.88    7.20
  23 GU/UG   -0.93   -5.19    0.60   -0.36   -5.24    0.05

(this structure has x on for a step without a continuous backbone- from the DSSR output; 3dna just leaves them blank)


    step       Xp      Yp      Zp     XpH     YpH     ZpH    Form
   1 ga/TC   -2.77    8.59    0.69   -3.28    8.62    0.28
   2 ac/GT   -2.49    8.71    1.70   -4.62    8.57    2.22
   3 ca/TG   -3.29    8.69    1.01   -7.71    7.93    3.84
   4 ac/GT   -3.02    9.01    1.11   -8.02    8.96    1.50
   5 cc/GG   -1.93    8.22    2.51   -5.41    7.78    3.66     A
   6 cu/AG   -2.26    8.95    1.99   -6.31    9.06    1.61     A
   7 ug/CA   -2.51    8.67    1.19   -4.74    8.70    1.07
   8 ga/uC   -2.43    8.87    1.41   -6.30    7.97    4.14
   9 au/Au   -2.90    8.63    0.53   -5.39    8.55    1.15
  10 uu/AA   -2.76    8.87    1.25   -8.18    8.07    3.92
  11 uc/GA   -2.38    8.52    1.92   -5.00    8.39    2.38


9 percent A..?



3DNA has been incredible to use so far, very multi-dimensional and comprehensive.
Thank you.


Offline Puru@1998

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Re: Classifying structures into A, B , AB, TA .. types
« Reply #4 on: July 04, 2018, 11:40:08 pm »
Hello.

I was wondering if you had a response regarding my post above.

Thanks.

Offline xiangjun

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Re: Classifying structures into A, B , AB, TA .. types
« Reply #5 on: July 05, 2018, 06:24:13 am »
Sorry for being late in responding to your follow-up post on June 22, 2018. I was on a trip to China for the whole month of June and slightly beyond, and I was constrained by my schedule and limited internet access.

Now back to your question, I am confused by what you mean by the following quantitative measures:

Quote
trying to classify structures as A ( 75-100 percent = A , 57/58- 75 percent = A-like , 43% - 58% = A to B)...
About 63 percent B so, B- Like...
9 percent A..?

The classification of a DNA dinucleotide step as A-, B- or TA-type is (mostly) based on Zp. See the 2000 A-DNA motif paper in JMB, and the 3DNA source code (ana_fncs.c) for further details.

Best regards,

Xiang-Jun
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], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.