DrawTetrado is a Python application to visualize quadruplexes and G4-helices in DNA and RNA structures. It generates publication-quality SVG files containing layer diagrams. They show the tetrads as a stack, with each position having four nucleobases colored according to anti or syn conformation. In addition, DrawTetrado visualizes the strands with arrows for an accessible overview of their directionality and visual determination of loop types.
DrawTetrado automatically optimizes the layout. The result is a visually pleasing and readable image, even for the most complex cases like V-loops and G4-helices (dimers).
pip install drawtetrado
The project is written in Python 3.6+ and requires pycairo, svgwrite, and orjson and ElTetrado (Zok et al., 2022; Popenda et al., 2020; Zok et al., 2020). The internal optimization routine is written in C++ and requires Cython and a C++20-compliant compiler (e.g. GCC 8+).
DrawTetrado parses the output of ElTetrado. It can also process PDB or PDBx/mmCIF files which will be first analyzed internally with ElTetrado.
usage: drawtetrado [-h] [-i INPUT] [-o OUTPUT_TEMPLATE] [--config CONFIG]
[-m MODEL] [--stacking-mismatch STACKING_MISMATCH] [--strict]
[--no-reorder]
options:
-h, --help show this help message and exit
-i INPUT, --input INPUT
path to input PDB, PDBx/mmCIF file or JSON generated by
ElTetrado. If PDB or PDBx/mmCIF file is provided, it will
be first analyzed using ElTetrado.
-o OUTPUT_TEMPLATE, --output-template OUTPUT_TEMPLATE
(optional) path to output SVG file template
[default=input file path and basename]
--config CONFIG (optional) JSON config file containing all parameter
changes and individual nucleotide coloring overrides
-m MODEL, --model MODEL
(optional, ElTetrado) model number to process
--stacking-mismatch STACKING_MISMATCH
(optional, ElTetrado) a perfect tetrad stacking covers 4
nucleotides; this option can be used with values 1 or 2 to
allow this number of nucleotides to be non-stacked with
otherwise well aligned tetrad [default=2]
--strict (optional, ElTetrado) nucleotides in tetrad are found
when linked only by cWH pairing
--no-reorder (optional, ElTetrado) chains of bi- and tetramolecular
quadruplexes should be reordered to be able to have them
classified; when this is set, chains will be processed in
the original order, which for bi-/tetramolecular means that
they will likely be misclassified; use with care!
The output path is a template. The program will generate drawings for each individual
quadruplex in each helix as well as each full helix. If we have a file with 2
helices with 2 quadruplexes each, if no output_template value is provided, path
and basename of the input file will be used. If it is provided,
output_template=/tmp/out, the resulting files will be /tmp/out_0.svg, with full
helix 0, /tmp/out_0_0.svg and /tmp/out_0_1.svg for each quadruplex in helix 0.
Similar files will be created for helix 1 with /tmp/out_1.svg and
/tmp/out_1_0.svg, /tmp/out_1_1.svg.
DrawTetrado allows for a wide variety of changes to the visual representation of the resulting drawing.
All modifications to visual aspects of the drawing can be done using JSON formatted config file. Example config.json is available in the repository with all possible parameters and their default values.
{
"_comment0": "Example config.json with all available parameters default values.",
"_comment1": "All parameters explained in README",
"scale": 1.0,
"nucl-longer": 100.0,
"nucl-shorter": 70.0,
"nucl-spacing": 10.0,
"angle": 50.0,
"tetrad-spacing": 50.0,
"line-stroke": 3.0,
"point-size": 6.0,
"point-stroke": 2.0,
"se-label-spacing": 20.0,
"se-label-font-size": 24.0,
"font-family": "Arial, Helvetica",
"label-font-size": 20.0,
"tilted_labels": true,
"label-chain": true,
"label-nucl-name": true,
"label-nucl-fullname": true,
"label-number": true,
"_comment2": "Colors in RGBA hex. If only RGB is provided, alpha of 1.0 is used",
"_comment3": "for anything other than ONZ colors. Those default to 0.85.",
"colors": {
"connection": "#000000FF",
"border": "#E23D28FF",
"text": "#000000FF",
"point": "#FFFFFFFF",
"anti": "#FFFFFFFF",
"syn": "#000000FF",
"n/a": "#606060FF",
"onz_default": "#646464D9",
"o_plus": "#1F78B4D9",
"o_minus": "#A6CEE3D9",
"n_plus": "#33A02CD9",
"n_minus": "#B2DF8AD9",
"z_plus": "#FF7F00D9",
"z_minus": "#FDBF6FD9"
},
"_comment3": "dictionary of nucleotide full name to desired color in RGBA hex.",
"_comment4": "If only RGB is provided, alpha of 0.85 (aka. D9) is used.",
"_comment_example": "'A.DG12': '#E23D28AA'",
"nucl-color-override": {}
}Nucleotide labels are made from 3 parts:
A.DG12
A - Chain of the nucleotide. If label-chain is set to false, this information (and .)
is not included in the creation of the labels.
DG - Full name of the nucleotide. Setting label-nucl-fullname to false will result
in normal short names like A, C, T, G. label-nucl-name to false will remove
nucleotide name part altogether.
12 - Index of the nucleotide. Can be removed with label-number set to false.
Examples of how A.DG12 label would look like with different label options:
A.DG12 - Default - All label parameters as true.
A.G12 - "label-nucl-fullname": false
A.12 - "label-nucl-name": false
DG12 - "label-chain": false
A.DG - "label-number": false
A - "label-number": false, "label-nucleotide": false
Click to see the input JSON
{
"metals": [],
"nucleotides": [
{
"index": 1,
"model": 1,
"chain": "A",
"number": 1,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA1",
"shortName": "A",
"chi": 22.308,
"glycosidicBond": "syn"
},
{
"index": 2,
"model": 1,
"chain": "A",
"number": 2,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA2",
"shortName": "A",
"chi": -123.055,
"glycosidicBond": "anti"
},
{
"index": 3,
"model": 1,
"chain": "A",
"number": 3,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA3",
"shortName": "A",
"chi": -94.966,
"glycosidicBond": "anti"
},
{
"index": 4,
"model": 1,
"chain": "A",
"number": 4,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG4",
"shortName": "G",
"chi": 79.284,
"glycosidicBond": "syn"
},
{
"index": 5,
"model": 1,
"chain": "A",
"number": 5,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG5",
"shortName": "G",
"chi": -126.017,
"glycosidicBond": "anti"
},
{
"index": 6,
"model": 1,
"chain": "A",
"number": 6,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG6",
"shortName": "G",
"chi": -127.267,
"glycosidicBond": "anti"
},
{
"index": 7,
"model": 1,
"chain": "A",
"number": 7,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DT7",
"shortName": "T",
"chi": -63.108,
"glycosidicBond": "syn"
},
{
"index": 8,
"model": 1,
"chain": "A",
"number": 8,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DT8",
"shortName": "T",
"chi": -138.795,
"glycosidicBond": "anti"
},
{
"index": 9,
"model": 1,
"chain": "A",
"number": 9,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA9",
"shortName": "A",
"chi": -148.84,
"glycosidicBond": "anti"
},
{
"index": 10,
"model": 1,
"chain": "A",
"number": 10,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG10",
"shortName": "G",
"chi": 58.779,
"glycosidicBond": "syn"
},
{
"index": 11,
"model": 1,
"chain": "A",
"number": 11,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG11",
"shortName": "G",
"chi": -123.857,
"glycosidicBond": "anti"
},
{
"index": 12,
"model": 1,
"chain": "A",
"number": 12,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG12",
"shortName": "G",
"chi": -84.367,
"glycosidicBond": "syn"
},
{
"index": 13,
"model": 1,
"chain": "A",
"number": 13,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DT13",
"shortName": "T",
"chi": -30.819,
"glycosidicBond": "syn"
},
{
"index": 14,
"model": 1,
"chain": "A",
"number": 14,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DT14",
"shortName": "T",
"chi": -168.518,
"glycosidicBond": "anti"
},
{
"index": 15,
"model": 1,
"chain": "A",
"number": 15,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA15",
"shortName": "A",
"chi": -105.729,
"glycosidicBond": "anti"
},
{
"index": 16,
"model": 1,
"chain": "A",
"number": 16,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG16",
"shortName": "G",
"chi": 74.323,
"glycosidicBond": "syn"
},
{
"index": 17,
"model": 1,
"chain": "A",
"number": 17,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG17",
"shortName": "G",
"chi": 81.084,
"glycosidicBond": "syn"
},
{
"index": 18,
"model": 1,
"chain": "A",
"number": 18,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG18",
"shortName": "G",
"chi": -122.904,
"glycosidicBond": "anti"
},
{
"index": 19,
"model": 1,
"chain": "A",
"number": 19,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DT19",
"shortName": "T",
"chi": -102.982,
"glycosidicBond": "anti"
},
{
"index": 20,
"model": 1,
"chain": "A",
"number": 20,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DT20",
"shortName": "T",
"chi": -112.151,
"glycosidicBond": "anti"
},
{
"index": 21,
"model": 1,
"chain": "A",
"number": 21,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA21",
"shortName": "A",
"chi": -89.071,
"glycosidicBond": "syn"
},
{
"index": 22,
"model": 1,
"chain": "A",
"number": 22,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG22",
"shortName": "G",
"chi": 83.443,
"glycosidicBond": "syn"
},
{
"index": 23,
"model": 1,
"chain": "A",
"number": 23,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG23",
"shortName": "G",
"chi": -115.412,
"glycosidicBond": "anti"
},
{
"index": 24,
"model": 1,
"chain": "A",
"number": 24,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG24",
"shortName": "G",
"chi": -111.148,
"glycosidicBond": "anti"
},
{
"index": 25,
"model": 1,
"chain": "A",
"number": 25,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA25",
"shortName": "A",
"chi": -58.324,
"glycosidicBond": "syn"
},
{
"index": 26,
"model": 1,
"chain": "A",
"number": 26,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA26",
"shortName": "A",
"chi": -90.841,
"glycosidicBond": "anti"
}
],
"basePairs": [
{
"nt1": "A.DA2",
"nt2": "A.DT20",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DT20",
"nt2": "A.DA2",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DA3",
"nt2": "A.DA21",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DA21",
"nt2": "A.DA3",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG4",
"nt2": "A.DT7",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DT7",
"nt2": "A.DG4",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG4",
"nt2": "A.DG10",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG10",
"nt2": "A.DG4",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG4",
"nt2": "A.DG22",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG22",
"nt2": "A.DG4",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG5",
"nt2": "A.DG11",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG11",
"nt2": "A.DG5",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG5",
"nt2": "A.DG23",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG23",
"nt2": "A.DG5",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG6",
"nt2": "A.DG12",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG12",
"nt2": "A.DG6",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG6",
"nt2": "A.DG24",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG24",
"nt2": "A.DG6",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DT7",
"nt2": "A.DG10",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "A.DG10",
"nt2": "A.DT7",
"stericity": "cis",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG10",
"nt2": "A.DG18",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG18",
"nt2": "A.DG10",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG11",
"nt2": "A.DG17",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG17",
"nt2": "A.DG11",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG12",
"nt2": "A.DG16",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG16",
"nt2": "A.DG12",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DT14",
"nt2": "A.DA25",
"stericity": "trans",
"edge5": "Watson-Crick",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DA25",
"nt2": "A.DT14",
"stericity": "trans",
"edge5": "Watson-Crick",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DA15",
"nt2": "A.DA25",
"stericity": "trans",
"edge5": "Sugar",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DA25",
"nt2": "A.DA15",
"stericity": "trans",
"edge5": "Watson-Crick",
"edge3": "Sugar"
},
{
"nt1": "A.DG16",
"nt2": "A.DG24",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG24",
"nt2": "A.DG16",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG17",
"nt2": "A.DG23",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG23",
"nt2": "A.DG17",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG18",
"nt2": "A.DG22",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG22",
"nt2": "A.DG18",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
}
],
"helices": [
{
"quadruplexes": [
{
"tetrads": [
{
"id": "A.DG6-A.DG12-A.DG16-A.DG24",
"nt1": "A.DG6",
"nt2": "A.DG12",
"nt3": "A.DG16",
"nt4": "A.DG24",
"onz": "O+",
"gbaClassification": "VIa",
"planarityDeviation": 0.1829350977806063,
"ionsChannel": [],
"ionsOutside": []
},
{
"id": "A.DG5-A.DG11-A.DG17-A.DG23",
"nt1": "A.DG5",
"nt2": "A.DG11",
"nt3": "A.DG17",
"nt4": "A.DG23",
"onz": "O+",
"gbaClassification": "Va",
"planarityDeviation": 0.10474313820007491,
"ionsChannel": [],
"ionsOutside": []
},
{
"id": "A.DG4-A.DG22-A.DG18-A.DG10",
"nt1": "A.DG4",
"nt2": "A.DG22",
"nt3": "A.DG18",
"nt4": "A.DG10",
"onz": "O-",
"gbaClassification": "Vb",
"planarityDeviation": 0.17372283960377813,
"ionsChannel": [],
"ionsOutside": []
}
],
"onzm": "Oh*",
"loopClassification": "9a",
"gbaClassification": ["V", "VI"],
"tracts": [
["A.DG16", "A.DG17", "A.DG18"],
["A.DG24", "A.DG23", "A.DG22"],
["A.DG6", "A.DG5", "A.DG4"],
["A.DG12", "A.DG11", "A.DG10"]
],
"loops": [
{
"type": "propeller-",
"nucleotides": ["A.DT7", "A.DT8", "A.DA9"]
},
{
"type": "lateral-",
"nucleotides": ["A.DT13", "A.DT14", "A.DA15"]
},
{
"type": "lateral+",
"nucleotides": ["A.DT19", "A.DT20", "A.DA21"]
}
]
}
],
"tetradPairs": [
{
"tetrad1": "A.DG6-A.DG12-A.DG16-A.DG24",
"tetrad2": "A.DG5-A.DG11-A.DG17-A.DG23",
"direction": "hybrid",
"rise": 3.1149939255558747,
"twist": 27.111587838260725
},
{
"tetrad1": "A.DG5-A.DG11-A.DG17-A.DG23",
"tetrad2": "A.DG4-A.DG22-A.DG18-A.DG10",
"direction": "hybrid",
"rise": 3.2109650905140654,
"twist": 20.409525129779524
}
]
}
]
}
Click to see the input JSON
{
"metals": [],
"nucleotides": [
{
"index": 1,
"model": 1,
"chain": "A",
"number": 1,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG1",
"shortName": "G",
"chi": 54.111,
"glycosidicBond": "syn"
},
{
"index": 2,
"model": 1,
"chain": "A",
"number": 2,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG2",
"shortName": "G",
"chi": 83.093,
"glycosidicBond": "syn"
},
{
"index": 3,
"model": 1,
"chain": "A",
"number": 3,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG3",
"shortName": "G",
"chi": -120.17,
"glycosidicBond": "anti"
},
{
"index": 4,
"model": 1,
"chain": "A",
"number": 4,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA4",
"shortName": "A",
"chi": -111.874,
"glycosidicBond": "anti"
},
{
"index": 5,
"model": 1,
"chain": "A",
"number": 5,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DT5",
"shortName": "T",
"chi": -153.281,
"glycosidicBond": "anti"
},
{
"index": 6,
"model": 1,
"chain": "A",
"number": 6,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG6",
"shortName": "G",
"chi": -106.483,
"glycosidicBond": "anti"
},
{
"index": 7,
"model": 1,
"chain": "A",
"number": 7,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG7",
"shortName": "G",
"chi": -122.668,
"glycosidicBond": "anti"
},
{
"index": 8,
"model": 1,
"chain": "A",
"number": 8,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG8",
"shortName": "G",
"chi": -125.241,
"glycosidicBond": "anti"
},
{
"index": 9,
"model": 1,
"chain": "A",
"number": 9,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA9",
"shortName": "A",
"chi": -90.027,
"glycosidicBond": "anti"
},
{
"index": 10,
"model": 1,
"chain": "A",
"number": 10,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DC10",
"shortName": "C",
"chi": -144.141,
"glycosidicBond": "anti"
},
{
"index": 11,
"model": 1,
"chain": "A",
"number": 11,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA11",
"shortName": "A",
"chi": -139.299,
"glycosidicBond": "anti"
},
{
"index": 12,
"model": 1,
"chain": "A",
"number": 12,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DC12",
"shortName": "C",
"chi": -89.925,
"glycosidicBond": "syn"
},
{
"index": 13,
"model": 1,
"chain": "A",
"number": 13,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA13",
"shortName": "A",
"chi": -116.926,
"glycosidicBond": "anti"
},
{
"index": 14,
"model": 1,
"chain": "A",
"number": 14,
"icode": " ",
"molecule": "Other",
"fullName": "A.GF2/14",
"shortName": "g",
"chi": 75.041,
"glycosidicBond": "syn"
},
{
"index": 15,
"model": 1,
"chain": "A",
"number": 15,
"icode": " ",
"molecule": "Other",
"fullName": "A.GFL15",
"shortName": "g",
"chi": -167.524,
"glycosidicBond": "anti"
},
{
"index": 16,
"model": 1,
"chain": "A",
"number": 16,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG16",
"shortName": "G",
"chi": -100.43,
"glycosidicBond": "anti"
},
{
"index": 17,
"model": 1,
"chain": "A",
"number": 17,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG17",
"shortName": "G",
"chi": -140.143,
"glycosidicBond": "anti"
},
{
"index": 18,
"model": 1,
"chain": "A",
"number": 18,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA18",
"shortName": "A",
"chi": -100.903,
"glycosidicBond": "anti"
},
{
"index": 19,
"model": 1,
"chain": "A",
"number": 19,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DC19",
"shortName": "C",
"chi": -131.147,
"glycosidicBond": "anti"
},
{
"index": 20,
"model": 1,
"chain": "A",
"number": 20,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG20",
"shortName": "G",
"chi": -169.165,
"glycosidicBond": "anti"
},
{
"index": 21,
"model": 1,
"chain": "A",
"number": 21,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG21",
"shortName": "G",
"chi": -105.18,
"glycosidicBond": "anti"
},
{
"index": 22,
"model": 1,
"chain": "A",
"number": 22,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG22",
"shortName": "G",
"chi": -106.1,
"glycosidicBond": "anti"
}
],
"basePairs": [
{
"nt1": "A.DG1",
"nt2": "A.DG7",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG7",
"nt2": "A.DG1",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG1",
"nt2": "A.DG16",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG16",
"nt2": "A.DG1",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG2",
"nt2": "A.DG6",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG6",
"nt2": "A.DG2",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG2",
"nt2": "A.GFL15",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.GFL15",
"nt2": "A.DG2",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG3",
"nt2": "A.DG6",
"stericity": "cis",
"edge5": "Sugar",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG6",
"nt2": "A.DG3",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Sugar"
},
{
"nt1": "A.DG3",
"nt2": "A.DG20",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG20",
"nt2": "A.DG3",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG6",
"nt2": "A.DG20",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG20",
"nt2": "A.DG6",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG7",
"nt2": "A.DG21",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG21",
"nt2": "A.DG7",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG8",
"nt2": "A.GF2/14",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.GF2/14",
"nt2": "A.DG8",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG8",
"nt2": "A.DG22",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG22",
"nt2": "A.DG8",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DC12",
"nt2": "A.DA13",
"stericity": "cis",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DA13",
"nt2": "A.DC12",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "A.GF2/14",
"nt2": "A.DG17",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG17",
"nt2": "A.GF2/14",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.GFL15",
"nt2": "A.DG20",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG20",
"nt2": "A.GFL15",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG16",
"nt2": "A.DA18",
"stericity": "trans",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DA18",
"nt2": "A.DG16",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "A.DG16",
"nt2": "A.DG21",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG21",
"nt2": "A.DG16",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG17",
"nt2": "A.DG22",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG22",
"nt2": "A.DG17",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
}
],
"helices": [
{
"quadruplexes": [
{
"tetrads": [
{
"id": "A.DG2-A.GFL15-A.DG20-A.DG6",
"nt1": "A.DG2",
"nt2": "A.GFL15",
"nt3": "A.DG20",
"nt4": "A.DG6",
"onz": "N-",
"gbaClassification": "VIIb",
"planarityDeviation": 0.2180730955436729,
"ionsChannel": [],
"ionsOutside": []
},
{
"id": "A.DG1-A.DG16-A.DG21-A.DG7",
"nt1": "A.DG1",
"nt2": "A.DG16",
"nt3": "A.DG21",
"nt4": "A.DG7",
"onz": "N-",
"gbaClassification": "VIIb",
"planarityDeviation": 0.23623267132215198,
"ionsChannel": [],
"ionsOutside": []
},
{
"id": "A.DG8-A.GF2/14-A.DG17-A.DG22",
"nt1": "A.DG8",
"nt2": "A.GF2/14",
"nt3": "A.DG17",
"nt4": "A.DG22",
"onz": "O+",
"gbaClassification": "IIIa",
"planarityDeviation": 0.12292426530184954,
"ionsChannel": [],
"ionsOutside": []
}
],
"onzm": "Mh*",
"loopClassification": "7b",
"gbaClassification": ["III", "VII"],
"tracts": [
["A.DG20", "A.DG21", "A.DG22"],
["A.DG6", "A.DG7", "A.DG8"],
["A.DG2", "A.DG1", "A.GF2/14"],
["A.GFL15", "A.DG16", "A.DG17"]
],
"loops": [
{
"type": "lateral+",
"nucleotides": ["A.DG3", "A.DA4", "A.DT5"]
},
{
"type": "lateral-",
"nucleotides": ["A.DA9", "A.DC10", "A.DA11", "A.DC12", "A.DA13"]
},
{
"type": "propeller-",
"nucleotides": ["A.DA18", "A.DC19"]
}
]
}
],
"tetradPairs": [
{
"tetrad1": "A.DG2-A.GFL15-A.DG20-A.DG6",
"tetrad2": "A.DG1-A.DG16-A.DG21-A.DG7",
"direction": "hybrid",
"rise": 3.4053905200064882,
"twist": 32.09137702765124
},
{
"tetrad1": "A.DG1-A.DG16-A.DG21-A.DG7",
"tetrad2": "A.DG8-A.GF2/14-A.DG17-A.DG22",
"direction": "parallel",
"rise": 3.4862467282164604,
"twist": 29.215089333872314
}
]
}
]
}
Click to see the input JSON
{
"metals": [],
"nucleotides": [
{
"index": 1,
"model": 1,
"chain": "A",
"number": 1,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG1",
"shortName": "G",
"chi": -109.42,
"glycosidicBond": "anti"
},
{
"index": 2,
"model": 1,
"chain": "A",
"number": 2,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG2",
"shortName": "G",
"chi": -128.871,
"glycosidicBond": "anti"
},
{
"index": 3,
"model": 1,
"chain": "A",
"number": 3,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA3",
"shortName": "A",
"chi": -56.59,
"glycosidicBond": "syn"
},
{
"index": 4,
"model": 1,
"chain": "A",
"number": 4,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG4",
"shortName": "G",
"chi": -171.001,
"glycosidicBond": "anti"
},
{
"index": 5,
"model": 1,
"chain": "A",
"number": 5,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG5",
"shortName": "G",
"chi": -127.906,
"glycosidicBond": "anti"
},
{
"index": 6,
"model": 1,
"chain": "A",
"number": 6,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA6",
"shortName": "A",
"chi": -87.061,
"glycosidicBond": "syn"
},
{
"index": 7,
"model": 1,
"chain": "A",
"number": 7,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG7",
"shortName": "G",
"chi": -159.577,
"glycosidicBond": "anti"
},
{
"index": 8,
"model": 1,
"chain": "A",
"number": 8,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG8",
"shortName": "G",
"chi": -135.751,
"glycosidicBond": "anti"
},
{
"index": 9,
"model": 1,
"chain": "A",
"number": 9,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA9",
"shortName": "A",
"chi": -50.982,
"glycosidicBond": "syn"
},
{
"index": 10,
"model": 1,
"chain": "A",
"number": 10,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG10",
"shortName": "G",
"chi": -135.29,
"glycosidicBond": "anti"
},
{
"index": 11,
"model": 1,
"chain": "A",
"number": 11,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DG11",
"shortName": "G",
"chi": -113.575,
"glycosidicBond": "anti"
},
{
"index": 12,
"model": 1,
"chain": "A",
"number": 12,
"icode": " ",
"molecule": "DNA",
"fullName": "A.DA12",
"shortName": "A",
"chi": -110.595,
"glycosidicBond": "anti"
},
{
"index": 13,
"model": 1,
"chain": "B",
"number": 13,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DG13",
"shortName": "G",
"chi": -112.685,
"glycosidicBond": "anti"
},
{
"index": 14,
"model": 1,
"chain": "B",
"number": 14,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DG14",
"shortName": "G",
"chi": -136.989,
"glycosidicBond": "anti"
},
{
"index": 15,
"model": 1,
"chain": "B",
"number": 15,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DA15",
"shortName": "A",
"chi": -57.076,
"glycosidicBond": "syn"
},
{
"index": 16,
"model": 1,
"chain": "B",
"number": 16,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DG16",
"shortName": "G",
"chi": -169.156,
"glycosidicBond": "anti"
},
{
"index": 17,
"model": 1,
"chain": "B",
"number": 17,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DG17",
"shortName": "G",
"chi": -124.27,
"glycosidicBond": "anti"
},
{
"index": 18,
"model": 1,
"chain": "B",
"number": 18,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DA18",
"shortName": "A",
"chi": -84.463,
"glycosidicBond": "syn"
},
{
"index": 19,
"model": 1,
"chain": "B",
"number": 19,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DG19",
"shortName": "G",
"chi": -164.508,
"glycosidicBond": "anti"
},
{
"index": 20,
"model": 1,
"chain": "B",
"number": 20,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DG20",
"shortName": "G",
"chi": -141.652,
"glycosidicBond": "anti"
},
{
"index": 21,
"model": 1,
"chain": "B",
"number": 21,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DA21",
"shortName": "A",
"chi": -59.955,
"glycosidicBond": "syn"
},
{
"index": 22,
"model": 1,
"chain": "B",
"number": 22,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DG22",
"shortName": "G",
"chi": -128.818,
"glycosidicBond": "anti"
},
{
"index": 23,
"model": 1,
"chain": "B",
"number": 23,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DG23",
"shortName": "G",
"chi": -108.407,
"glycosidicBond": "anti"
},
{
"index": 24,
"model": 1,
"chain": "B",
"number": 24,
"icode": " ",
"molecule": "DNA",
"fullName": "B.DA24",
"shortName": "A",
"chi": -115.199,
"glycosidicBond": "anti"
}
],
"basePairs": [
{
"nt1": "A.DG1",
"nt2": "A.DA3",
"stericity": "trans",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DA3",
"nt2": "A.DG1",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "A.DG1",
"nt2": "A.DG4",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG4",
"nt2": "A.DG1",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG1",
"nt2": "A.DG10",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG10",
"nt2": "A.DG1",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG2",
"nt2": "A.DG5",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG5",
"nt2": "A.DG2",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG2",
"nt2": "A.DG11",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG11",
"nt2": "A.DG2",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG2",
"nt2": "A.DA12",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DA12",
"nt2": "A.DG2",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DA3",
"nt2": "A.DG4",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG4",
"nt2": "A.DA3",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG4",
"nt2": "A.DA6",
"stericity": "cis",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DA6",
"nt2": "A.DG4",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "A.DG4",
"nt2": "A.DG7",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG7",
"nt2": "A.DG4",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG4",
"nt2": "B.DG22",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG22",
"nt2": "A.DG4",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG5",
"nt2": "A.DG8",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG8",
"nt2": "A.DG5",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DA6",
"nt2": "A.DG7",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG7",
"nt2": "A.DA6",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG7",
"nt2": "A.DA9",
"stericity": "trans",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DA9",
"nt2": "A.DG7",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "A.DG7",
"nt2": "A.DG10",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG10",
"nt2": "A.DG7",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG8",
"nt2": "A.DG11",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG11",
"nt2": "A.DG8",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG8",
"nt2": "A.DA12",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DA12",
"nt2": "A.DG8",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.DG10",
"nt2": "B.DG16",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG16",
"nt2": "A.DG10",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "A.DG10",
"nt2": "B.DG22",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Watson-Crick"
},
{
"nt1": "B.DG22",
"nt2": "A.DG10",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Watson-Crick"
},
{
"nt1": "B.DG13",
"nt2": "B.DA15",
"stericity": "trans",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DA15",
"nt2": "B.DG13",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "B.DG13",
"nt2": "B.DG16",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG16",
"nt2": "B.DG13",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.DG13",
"nt2": "B.DG22",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.DG22",
"nt2": "B.DG13",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG14",
"nt2": "B.DG17",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG17",
"nt2": "B.DG14",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.DG14",
"nt2": "B.DG23",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.DG23",
"nt2": "B.DG14",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG14",
"nt2": "B.DA24",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.DA24",
"nt2": "B.DG14",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DA15",
"nt2": "B.DG16",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG16",
"nt2": "B.DA15",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG16",
"nt2": "B.DA18",
"stericity": "cis",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DA18",
"nt2": "B.DG16",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "B.DG16",
"nt2": "B.DG19",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG19",
"nt2": "B.DG16",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.DG17",
"nt2": "B.DG20",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG20",
"nt2": "B.DG17",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.DA18",
"nt2": "B.DG19",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG19",
"nt2": "B.DA18",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG19",
"nt2": "B.DA21",
"stericity": "trans",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DA21",
"nt2": "B.DG19",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "B.DG19",
"nt2": "B.DG22",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG22",
"nt2": "B.DG19",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.DG20",
"nt2": "B.DG23",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.DG23",
"nt2": "B.DG20",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
}
],
"helices": [
{
"quadruplexes": [
{
"tetrads": [
{
"id": "B.DG14-B.DG17-B.DG20-B.DG23",
"nt1": "B.DG14",
"nt2": "B.DG17",
"nt3": "B.DG20",
"nt4": "B.DG23",
"onz": "O+",
"gbaClassification": "VIIIa",
"planarityDeviation": 0.16023147318800904,
"ionsChannel": [],
"ionsOutside": []
},
{
"id": "B.DG13-B.DG16-B.DG19-B.DG22",
"nt1": "B.DG13",
"nt2": "B.DG16",
"nt3": "B.DG19",
"nt4": "B.DG22",
"onz": "O+",
"gbaClassification": "VIIIa",
"planarityDeviation": 0.45582726991701444,
"ionsChannel": [],
"ionsOutside": []
}
],
"onzm": "Op+",
"loopClassification": "1a",
"gbaClassification": ["VIII"],
"tracts": [
["B.DG23", "B.DG22"],
["B.DG14", "B.DG13"],
["B.DG17", "B.DG16"],
["B.DG20", "B.DG19"]
],
"loops": [
{
"type": "propeller-",
"nucleotides": ["B.DA15"]
},
{
"type": "propeller-",
"nucleotides": ["B.DA18"]
},
{
"type": "propeller-",
"nucleotides": ["B.DA21"]
}
]
},
{
"tetrads": [
{
"id": "A.DG1-A.DG4-A.DG7-A.DG10",
"nt1": "A.DG1",
"nt2": "A.DG4",
"nt3": "A.DG7",
"nt4": "A.DG10",
"onz": "O+",
"gbaClassification": "VIIIa",
"planarityDeviation": 0.5675509888987945,
"ionsChannel": [],
"ionsOutside": []
},
{
"id": "A.DG2-A.DG5-A.DG8-A.DA12",
"nt1": "A.DG2",
"nt2": "A.DG5",
"nt3": "A.DG8",
"nt4": "A.DA12",
"onz": "O+",
"gbaClassification": "VIIIa",
"planarityDeviation": 0.7820234571290057,
"ionsChannel": [],
"ionsOutside": []
}
],
"onzm": "Op+",
"loopClassification": "1a",
"gbaClassification": ["VIII"],
"tracts": [
["A.DG7", "A.DG8"],
["A.DG10", "A.DA12"],
["A.DG1", "A.DG2"],
["A.DG4", "A.DG5"]
],
"loops": [
{
"type": "propeller-",
"nucleotides": ["A.DA3"]
},
{
"type": "propeller-",
"nucleotides": ["A.DA6"]
},
{
"type": "propeller-",
"nucleotides": ["A.DA9"]
}
]
}
],
"tetradPairs": [
{
"tetrad1": "B.DG14-B.DG17-B.DG20-B.DG23",
"tetrad2": "B.DG13-B.DG16-B.DG19-B.DG22",
"direction": "parallel",
"rise": 3.4598098620083153,
"twist": 26.65295578601502
},
{
"tetrad1": "B.DG13-B.DG16-B.DG19-B.DG22",
"tetrad2": "A.DG1-A.DG4-A.DG7-A.DG10",
"direction": "parallel",
"rise": 3.1498276292124316,
"twist": 7.769329062763674
},
{
"tetrad1": "A.DG1-A.DG4-A.DG7-A.DG10",
"tetrad2": "A.DG2-A.DG5-A.DG8-A.DA12",
"direction": "parallel",
"rise": 4.363977409213413,
"twist": 53.69239641441069
}
]
}
]
}-
ONQUADRO: a database of experimentally determined quadruplex structures. T. Zok, N. Kraszewska, J. Miskiewicz, P. Pielacinska, M. Zurkowski, M. Szachniuk. Nucleic Acids Research. 2022. 50(D1):D253–D258. doi:10.1093/nar/gkab1118
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Topology-based classification of tetrads and quadruplex structures. M. Popenda, J. Miskiewicz, J. Sarzynska, T. Zok, M. Szachniuk. Bioinformatics. 2020. 36(4):1129–1134. doi:10.1093/bioinformatics/btz738
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ElTetrado: a tool for identification and classification of tetrads and quadruplexes. T. Zok, M. Popenda, M. Szachniuk. BMC Bioinformatics. 2020. 21(1):40. doi:10.1186/s12859-020-3385-1