Recent Posts

1

General discussions (Q&As) / Re: Add C or T to 5' end of an RNA bound to QKI PDB file

« Last post by xiangjun on July 14, 2018, 05:18:50 pm »

Thanks for such a well-phrased question! Yes, 3DNA/DSSR has some utilities that may help in achieving your goal.

4JVH.pdb (QKI) http://www.rcsb.org/structure/4JVH has the RNA ACUAACAA and I need to trim that to _ACUAAC because that lines up the best with YNCURAY.  The underscore needs to be the C or T and to do that I need 3DNA to add the C or T to the 5' end of the ACUAAC.

I assume the conformation of the 5' C or T to be added is not defined, i.e. it can be any (reasonable) starting geometry. You could use frame_mol to set the ACUAAC fragment from 4JVH to be in the base reference of the first A. You can choose any (or your favorite) CA (or TA) dinucleotide from the PDB, and use the same frame_mol utility to reset it to the base reference frame of the ending A. Since both the ACUAAC fragment and the CA fragment share the same A base reference frame, you can overlay them together. With some manual editing, you should be able to get an approximate starting PDB structure with required RNA base sequence for your MD simulations.

Have a try and let me know if it works.

Xiang-Jun

2

General discussions (Q&As) / Add C or T to 5' end of an RNA bound to QKI PDB file

« Last post by Hari Seldon on July 14, 2018, 03:36:45 pm »

Does 3DNA have a function to add a nucleotide to the 5' end of an RNA in a pdb file?

My project is to search the transcriptome for more sites that the RNA-binding proteins QKI and SF1 might compete.  We already know that they compete just upstream of Exon 12 of NUMB and if QKI wins it prevents SF1 from binding and prevents SF1 from recruiting the spliceosome there, so exon skipping of exon 12 happens.


I know the motif for the QKI dimer is NACUAAY-N(1-20)-UAAY and the motif for the SF1 monomer (it does not dimerize) is YNCURAY.  After I run molecular dynamics of QKI against the SF1 RNA motif I will compare the binding energies to see how well QKI binds against the SF1 motif to see how well QKI competes against SF1.

I have used 3DNA's mutate_bases in the past in this project, but now I need to add a C or T to the 5' end of the RNA bound to QKI, because 4JVH.pdb (QKI) http://www.rcsb.org/structure/4JVH has the RNA ACUAACAA and I need to trim that to _ACUAAC because that lines up the best with YNCURAY.  The underscore needs to be the C or T and to do that I need 3DNA to add the C or T to the 5' end of the ACUAAC.

3

General discussions (Q&As) / Re: Classifying structures into A, B , AB, TA .. types

« Last post by xiangjun 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:

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

4

General discussions (Q&As) / Re: Classifying structures into A, B , AB, TA .. types

« Last post by Puru@1998 on July 04, 2018, 11:40:08 pm »

Hello.

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

Thanks.

5

General discussions (Q&As) / Re: Classifying structures into A, B , AB, TA .. types

« Last post by Puru@1998 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.

6

General discussions (Q&As) / Re: Classifying structures into A, B , AB, TA .. types

« Last post by xiangjun on June 20, 2018, 01:29:06 pm »

Thanks, Mauricio, for chiming in and for your nice words about my early publications.

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

7

Programs / Re: blocview

« Last post by xiangjun on June 20, 2018, 01:21:05 pm »

Hi Mauricio,

Nice to see you again on the 3DNA Forum!

I would also like to change the radius of the sticks representing the sugar-phosphate backbone bonds.

The default radius of the sticks is set via the r3d_atom -r=0.16 option in the blocview script. See the excerpt below:

Code: Ruby

1.         # color nucleic-acid base/sugar by residue type
2.         Utils.run_cmd("#{$x3dna}r3d_atom -ncz -r=0.16 tb.pdb #{$temp_r3d} #{$msg}")
3.         Utils.append_r3dfile(opts[:r3dfile], $temp_r3d)

So you may change the radius 0.16 to your preferred value.

Alternatively (and preferably), you may want to give DSSR a try. DSSR has integrated blocview as a command-line option, and employes PyMOL for rendering. See the DSSR User Manual for more details.

HTH,

Xiang-Jun

 

8

Programs / blocview

« Last post by mauricio esguerra on June 20, 2018, 08:44:54 am »

Hi Xiang-Jun,

In using blocview I know that the radius of the backbone tube which traces the phosphate atoms can be changed in the last line of the $X3DNA/config/col_chain.dat file.

Nonetheless I would also like to change the radius of the sticks representing the sugar-phosphate backbone bonds.
I can do this manually by altering the resulting .r3d files, say, if one of these bond specifications as a cylinder in raster3D is:

Code: [Select]

3
  -10.965  -18.757   -1.704    0.160   -9.568  -18.592   -1.909    0.160    1.000    1.000    0.000

I can change the 0.160 value in the fourth and eight fields to whichever radius I want.
I was wondering if there's a file where this parameter can be changed in an easier way.

Thanks,

Mauricio

9

General discussions (Q&As) / Re: Classifying structures into A, B , AB, TA .. types

« Last post by mauricio esguerra 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

10

General discussions (Q&As) / Classifying structures into A, B , AB, TA .. types

« Last post by Puru@1998 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