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1
MD simulations / Re: Analysis of major groove and minor groove
« Last post by xiangjun on Today at 12:00:07 pm »
In 3DNA, the algorithm for characterizing minor and major groove widths of a DNA duplex is based on the 1998 JMB paper of El Hassan and Calladine, as shown below:

Quote
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.

More specifically, the "Appendix: Calculation of Major- and Minor-groove Widths" which is included in the 3DNA distribution ($X3DNA/doc/groove-widths.pdf). See 3DNA v2.x source code, if you want to get to the bottom of this issue.

HTH,

Xiang-Jun
2
MD simulations / Analysis of major groove and minor groove
« Last post by xroxzero on Today at 11:36:51 am »
Hi

About the analysis of major groove and minor groove , in this website ,
http://do-x3dna.readthedocs.io/en/latest/dna_class_api.html#dnaMD.dnaMD.DNA.set_major_minor_groove ,
it said that "The major and minor grooves (direct P-P) cannot be calculated for first and last two base-steps" .

Does any one know the reason why major and minor grooves cannot be calculated for first and last two base-steps ?


Thanks a lot
3
Quote
there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t

My question is whether DSSR can detect such ligand and RNA interaction?

No, in general. This feature is beyong DSSR’s design scope, at least for now. Why not using the result from reported from the RCSB PDB website? It is an ‘authoritative’ resource, isn't it?

Quote
Also, generally speaking, can DSSR detect protein/peptide and nucleic acid stacking interaction? For example, the stacking between aromatic ring of Phenylalanine and nucleic acid base?

You may find SNAP helpful. Again, do not forget the many other resources/tools in the field.

Xiang-Jun
4
Hi Xiangjun,

Also, generally speaking, can DSSR detect protein/peptide and nucleic acid stacking interaction? For example, the stacking between aromatic ring of Phenylalanine and nucleic acid base?

Best,
Honglue
5
Hi Xiangjun,

My new target structure is 1F1T from RCSB. It is a malachite green aptamer with a ligand called N,N'-TETRAMETHYL-ROSAMINE (ROS).
If you go to the PDB website and search for this PDB, you can see there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t

My question is whether DSSR can detect such ligand and RNA interaction?

Here, I also attach the PDB file and json file that I generated for your convenience.

Best,
Honglue



6
RNA structures (DSSR) / Re: Definition of Helix Form
« Last post by xiangjun on November 13, 2017, 02:39:09 pm »
Quote
PS. these data is under publication so I am not sure if I can provide further details but I will try my best to give you as much detain as you want.

I understand. Note also that the A-, B-, and Z-form classification algorithm implemented in DSSR is unpublished yet, as I mentioned previously. DSSR contains many undocumented features, which, if elaborated in combination with a survey of the PDB, could lead to solid publications. I've limited resources, and have to focus on the essence of DSSR as a whole. I'm glad to see that some users indeed have taken advantage of specific features of what DSSR has to offer. With collaborations, I may help to dig into some specific topics more thoroughly and efficiently.

I've no comment on your unpublished results. Since you're also using 3DNA v2.x, it helps to check the A- and B-form classification results from the analyze program. The fiber also contains the -rna option.

Xiang-Jun
7
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« Last post by xiangjun on November 13, 2017, 02:01:21 pm »
Quote
Is there any command to parse json if we have already generated the json file?

Sure. The pipe form is just a shorthand to avoid an intermediate file. You can certainly generate the JSON file first, and then parse it using jq -- see the excellent documentation of jq for examples.

Code: Ruby
  1. x3dna-dssr -i=3bnq.pdb --get-hbond --json | jq .hbonds[1]
  2.  
  3. # can be decomposed into the following two steps:
  4. x3dna-dssr -i=3bnq.pdb --get-hbond --json -o=3bnq-hbonds.json
  5. jq .hbonds[1] 3bnq-hbonds.json
  6.  
  7. # all with the following results:
  8. {
  9.   "index": 2,
  10.   "atom1_serNum": 59,
  11.   "atom2_serNum": 975,
  12.   "donAcc_type": "standard",
  13.   "distance": 2.532,
  14.   "atom1_id": "O6@A.G3",
  15.   "atom2_id": "N4@B.C23",
  16.   "atom_pair": "O:N",
  17.   "residue_pair": "nt:nt"
  18. }
  19.  

Xiang-Jun
8
RNA structures (DSSR) / Re: Bulge motif
« Last post by lvelve0901 on November 13, 2017, 11:07:40 am »
I understand.

Thanks.

Best,
Honglue
9
RNA structures (DSSR) / Re: Definition of Helix Form
« Last post by lvelve0901 on November 13, 2017, 11:06:08 am »
I actually did some work to benchmark whether 3DNA did a good job to identify the helix form.

In our lab, we have an in-hosue database of all the DNA stem and RNA stem structures from the entire crystal structures labeled "Protein#DNA" and "Protein#RNA" deposited in RCSB with resolution under 4Å. Yes, I use DSSR to generate stem structures for each PDB.

Then I build fiber idealized B form DNA and idealized A form RNA using 3DNA. If you type

fiber -m

It will generate a list of different nucleic acid model, I pick the number 4 for B-DNA and number 20 for A-RNA.

[hs189@summer:Plot] fiber -m
Fiber data in directory: /home/hs189/X3DNA/fiber/

id#  Twist   Rise        Structure description
   (degree) (Angstrom)
-------------------------------------------------------------------------------
 1   32.7   2.548  A-DNA  (calf thymus; generic sequence: A, C, G and T)
 2   65.5   5.095  A-DNA  poly d(ABr5U) : poly d(ABr5U)
 3    0.0  28.030  A-DNA  (calf thymus) poly d(A1T2C3G4G5A6A7T8G9G10T11) :
                                        poly d(A1C2C3A4T5T6C7C8G9A10T11)
 4   36.0   3.375  B-DNA  (calf thymus; generic sequence: A, C, G and T)
 5   72.0   6.720  B-DNA  poly d(CG) : poly d(CG)
 6  180.0  16.864  B-DNA  (calf thymus) poly d(C1C2C3C4C5) : poly d(G6G7G8G9G10)
 7   38.6   3.310  C-DNA  (calf thymus; generic sequence: A, C, G and T)
 8   40.0   3.312  C-DNA  poly d(GGT) : poly d(ACC)
 9  120.0   9.937  C-DNA  poly d(G1G2T3) : poly d(A4C5C6)
10   80.0   6.467  C-DNA  poly d(AG) : poly d(CT)
11   80.0   6.467  C-DNA  poly d(A1G2) : poly d(C3T4)
12   45.0   3.013  D-DNA  poly d(AAT) : poly d(ATT)
13   90.0   6.125  D-DNA  poly d(CI) : poly d(CI)
14  -90.0  18.500  D-DNA  poly d(A1T2A3T4A5T6) : poly d(A1T2A3T4A5T6)
15  -60.0   7.250  Z-DNA  poly d(GC) : poly d(GC)
16  -51.4   7.571  Z-DNA  poly d(As4T) : poly d(As4T)
17    0.0  10.200  L-DNA  (calf thymus) poly d(GC) : poly d(GC)
18   36.0   3.230  B'-DNA alpha poly d(A) : poly d(T) (H-DNA)
19   36.0   3.233  B'-DNA beta2 poly d(A) : poly d(T) (H-DNA  beta)
20   32.7   2.812  A-RNA  poly (A) : poly (U)


I know that the 3DNA identify the helix form in a dinucleotide step so I generated two base pair long idealized B-DNA and A-RNA to align the coordinate of the stem structures I generated using only backbone and sugar heavy atom and yielded an alignment RMSD for each dinucleotide step in my database.

Here is the result:

My RMSD cutoff is 2Å.

Protein#DNA
Total number of entries (dinucleotide step): 97366
Number of entries with RMSD (> 2Å) but 3DNA think it is B form: 49
Number of entries with RMSD (< 2Å) but 3DNA think it is X form (ambiguous): 29702
The rest of entries is 3DNA agree with my RMSD cut off.

Protein#RNA
Total number of entries (dinucleotide step): 56530
Number of entries with RMSD (> 2Å) but 3DNA think it is A form: 0
Number of entries with RMSD (< 2Å) but 3DNA think it is X form (ambiguous): 22893
The rest of entries is 3DNA agree with my RMSD cut off.

I think 3DNA basically did a good job considering the number of entries that excess the RMSD cutoff but 3DNA think it is A/B form among the entire PDB.
I am just wondering does 3DNA also simply use coordinate alignment to identify the helix form?

Best,
Honglue

PS. these data is under publication so I am not sure if I can provide further details but I will try my best to give you as much detain as you want.
10
RNA structures (DSSR) / Re: FRABASE
« Last post by lvelve0901 on November 13, 2017, 10:06:40 am »
I see.

Thanks.

Best,
Honglue
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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.