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Author Topic: NUPARM vs 3DNA  (Read 4619 times)

Offline prasun30

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NUPARM vs 3DNA
« on: October 09, 2015, 11:19:17 am »
Dear Forum

I was comparing the results of NUPARM with those of 3DNA, especially the inter
strand PP distances (NUPARM) and groove widths (3DNA).

While doing so, I was able to trace the major groove width in the PP distance
matrix, but was unsuccessful in the case of minor groove.

I took 1BNA as a test case. I am attaching the file containing groove widths and
PP distances.

When I calculated the distances between two phosphates using PyMol, NUPARM seems
to be giving correct values. Please let me know, where I am doing something
wrong.

My point is that the P-P distances given by the 3DNA and NUPARM, should be
matching to each other and I should be able to find them in the matrix.

Regards
Prasun Kumar

Offline xiangjun

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Re: NUPARM vs 3DNA
« Reply #1 on: October 09, 2015, 12:45:00 pm »
Hi Prasun Kumar,

Thanks for the 'bug report'. To facilitate our communications, I am putting your attached file in pre-formatted form (content of '1BNA_groove_width.txt').

Code: [Select]
3DNA
                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 CG/CG       ---       ---       ---       ---
   2 GC/GC       ---       ---       ---       ---
   3 CG/CG      13.8       ---      17.3       ---
   4 GA/TC      12.0      12.0      17.3      17.3
   5 AA/TT      10.5      10.5      17.5      17.3
   6 AT/AT       9.9       9.9      16.8      16.3
   7 TT/AA       9.3       9.3      17.4      17.4
   8 TC/GA      10.0       9.9      18.5      18.4
   9 CG/CG      11.0       ---      17.8       ---
  10 GC/GC       ---       ---       ---       ---
  11 CG/CG       ---       ---       ---       ---
 
NUPARM

  Inter-chain P--P distances
  Strand2: 5'-->3'
 Strand1:
PP     2. P   37.07  33.00  27.61  22.52  19.58  17.41  17.32  18.27  18.81  18.50  17.96
PP     3. P   33.23  28.47  22.91  18.57  17.60  17.32  18.20  18.97  19.06  18.14  16.78
PP     4. P   28.98  24.01  18.93  16.44  17.53  18.17  18.83  18.65  18.01  16.69  15.26
PP     5. P   24.78  20.34  16.72  16.78  19.03  19.50  19.12  17.57  16.15  14.93  14.53
PP     6. P   21.83  19.05  17.38  18.85  20.53  19.75  17.75  14.74  12.90  12.99  15.08
PP     7. P   19.29  18.48  18.10  19.58  19.92  17.82  14.65  11.31  11.06  14.25  18.78
PP     8. P   17.77  18.28  18.27  18.96  17.88  14.89  11.58   9.99  12.77  18.00  23.36
PP     9. P   17.75  18.70  18.30  17.57  14.86  11.49   9.77  11.98  17.01  22.92  28.24
PP    10. P   18.95  19.16  17.72  15.25  11.19   8.90  10.92  15.99  21.69  27.35  32.04
PP    11. P   17.96  17.84  16.43  13.95  11.05  12.32  16.60  22.04  27.50  32.70  36.77
PP    12. P   18.06  16.11  13.65  10.92  10.55  15.20  20.85  26.26  31.14  35.42  38.46

First, your reported 3DNA groove widths are correct. For other viewers of the Forum, one can easily analyze 1bna with 3DNA as follows:

Code: [Select]
find_pair 1bna.pdb 1bna.inp
analyze 1bna.inp
# or: find_pair 1bna.pdb stdout | analyze stdin

The main output file 1bna.out (attached) contains 3DNA parameters for the PDB entry 1bna.

Second, the section of 3DNA groove widths also includes a header, providing reference to the 1998 El Hassan and Calladine JMB paper. 3DNA implements the algorithm detailed in "Appendix: Calculation of Major- and Minor-groove Widths" of the paper.

Code: [Select]
****************************************************************************
Minor and major groove widths: direct P-P distances and refined P-P distances
   which take into account the directions of the sugar-phosphate backbones

   (Subtract 5.8 Angstrom from the values to take account of the vdw radii
    of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
     Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 CG/CG       ---       ---       ---       ---
   2 GC/GC       ---       ---       ---       ---
   3 CG/CG      13.8       ---      17.3       ---
   4 GA/TC      12.0      12.0      17.3      17.3
   5 AA/TT      10.5      10.5      17.5      17.3
   6 AT/AT       9.9       9.9      16.8      16.3
   7 TT/AA       9.3       9.3      17.4      17.4
   8 TC/GA      10.0       9.9      18.5      18.4
   9 CG/CG      11.0       ---      17.8       ---
  10 GC/GC       ---       ---       ---       ---
  11 CG/CG       ---       ---       ---       ---

Third, as shown in Eq. (A1) and Figure A1 of the El Hassan and Calladine JMB paper, "Accordingly, we define the minor-groove width for a step such as 4 in Figure A1(a) as the mean of the two marked distances". To make our discussion more concrete, the following image details how the the minor widths for dinucleotide steps 5 (AA/TT) and 6 (AT/AT) as reported in 3DNA come about.



Forth, 3DNA also creates a file named auxiliary.par (attached) which contains the following section:

Code: [Select]
Phosphorus-phosphorus distance in Angstroms

            1      2      3      4      5      6      7      8      9     10     11     12
            G      C      G      C      T      T      A      A      G      C      G      C   
   1 C    ----   ----   ----   ----   ----   ----   ----   ----   ----   ----   ----   ----
   2 G    18.0   18.5   18.8   18.3   17.3   17.4   19.6   22.5   27.6   33.0   37.1   ----
   3 C    16.8   18.1   19.1   19.0   18.2   17.3   17.6   18.6   22.9   28.5   33.2   ----
   4 G    15.3   16.7   18.0   18.6   18.8   18.2   17.5   16.4   18.9   24.0   29.0   ----
   5 A    14.5   14.9   16.1   17.6   19.1   19.5   19.0   16.8   16.7   20.3   24.8   ----
   6 A    15.1   13.0   12.9   14.7   17.8   19.7   20.5   18.8   17.4   19.0   21.8   ----
   7 T    18.8   14.3   11.1   11.3   14.6   17.8   19.9   19.6   18.1   18.5   19.3   ----
   8 T    23.4   18.0   12.8   10.0   11.6   14.9   17.9   19.0   18.3   18.3   17.8   ----
   9 C    28.2   22.9   17.0   12.0    9.8   11.5   14.9   17.6   18.3   18.7   17.7   ----
  10 G    32.0   27.3   21.7   16.0   10.9    8.9   11.2   15.3   17.7   19.2   19.0   ----
  11 C    36.8   32.7   27.5   22.0   16.6   12.3   11.0   14.0   16.4   17.8   18.0   ----
  12 G    38.5   35.4   31.1   26.3   20.8   15.2   10.6   10.9   13.7   16.1   18.1   ----
As you can see, this output agrees with NUPARM, except for differences in ordering and decimal points.

HTH,

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

Offline prasun30

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Re: NUPARM vs 3DNA
« Reply #2 on: October 09, 2015, 01:26:55 pm »
Dear Xiang

Thanx alot for the detailed and prompt reply. It is really helpful to me.
I was wondering if the web server can also give the "auxiliary.par" file (just for the download).
I did not find on the result page (sorry if I have overlooked it).

Regards
Prasun

Offline xiangjun

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Re: NUPARM vs 3DNA
« Reply #3 on: October 09, 2015, 01:34:19 pm »
Hi Prasun,

The w3DNA web server hosted at Rutgers do not necessarily make available all additional files the 3DNA analyze program generates. I am working on a new web interface to 3DNA, which should include such info. However, the updated 3DNA web-interface may not be ready until late this year.

You can always use the command-line version, which is not that hard to set up and use. Also, I am quick in answering any 3DNA-related questions on the Forum.

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

Offline prasun30

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Re: NUPARM vs 3DNA
« Reply #4 on: October 09, 2015, 02:17:51 pm »
Dear Xiang

Thanx alot for the suggestion. I will try using the command line.

Regards
Prasun

Offline xiangjun

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Re: NUPARM vs 3DNA
« Reply #5 on: October 09, 2015, 02:25:54 pm »
Hi Prasun,

While you are at it, you may also want to give DSSR a try. It is a representative of what'd become 3DNA v3.

Best regards,

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

Offline prasun30

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Re: NUPARM vs 3DNA
« Reply #6 on: October 10, 2015, 08:59:18 am »
Dear Xiang

Definitely I will.

Regards
Prasun

 

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.