Draw simplified, layer diagrams of quadruplexes.
Project description
Project description
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).
Installation
pip install drawtetrado
Dependencies
The project is written in Python 3.6+ and requires pycairo and svgwrite. 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 (Zok et al., 2022; Popenda et al., 2020; Zok et al., 2020). If you do not have that installed, please install DSSR (Lu et al., 2015) and run:
pip install eltetrado
Usage
usage: drawtetrado [-h] [--config CONFIG] input output_template
positional arguments:
input path to input JSON generated by ElTetrado
output_template path to output SVG file template
optional arguments:
-h, --help show this help message and exit
--config CONFIG JSON config file containing all parameter changes and
individual nucleotide coloring overrides
The output path is a template. Program will generate drawings for each
individual quadruplex in each helice as well as each full helice.If we have
file with 2 helices with 2 quadruplexes each, if output_template=/tmp/out.svg,
the resulting files will be /tmp/out_0.svg, with full helice 0,
/tmp/out_0_0.svg and /tmp/out_0_1.svg for each quadruplex in helice 0. Similar
files will be created for helice 1 with /tmp/out_1.svg and /tmp/out_1_0.svg,
/tmp/out_1_1.svg.
Visual customization
DrawTetrado allows for wide veriaty 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 respository 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
Examples
Human telomere DNA quadruplex
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
}
]
}
]
}
V-loop
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
}
]
}
]
}
G4-helix (dimer)
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
}
]
}
]
}
Bibliography
-
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
-
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
-
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
-
DSSR: an integrated software tool for dissecting the spatial structure of RNA. X.-J. Lu, H.J. Bussemaker, W.K. Olson. Nucleic Acids Research. 2015. 43(21):e142. doi:f73r8c
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